/*
* 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 jalview.analysis.AlignmentUtils;
import jalview.api.AlignFrameI;
import jalview.api.AlignViewportI;
import jalview.api.JalviewApp;
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.HiddenColumns;
import jalview.datamodel.PDBEntry;
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.NewickFile;
import jalview.javascript.JSFunctionExec;
import jalview.javascript.JalviewLiteJsApi;
import jalview.javascript.JsCallBack;
import jalview.javascript.MouseOverStructureListener;
import jalview.renderer.seqfeatures.FeatureRenderer;
import jalview.structure.SelectionListener;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
import jalview.util.ColorUtils;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
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.Vector;
import netscape.javascript.JSObject;
/**
* Jalview Applet. Runs in Java 1.18 runtime
*
* @author $author$
* @version $Revision: 1.92 $
*/
@SuppressWarnings("serial")
public class JalviewLite extends Applet
implements StructureSelectionManagerProvider, JalviewLiteJsApi,
JalviewApp
{
public JalviewLite()
{
appLoader = new JalviewAppLoader(debug);
}
private static final String TRUE = "true";
private static final String FALSE = "false";
public StructureSelectionManager getStructureSelectionManager()
{
return StructureSelectionManager.getStructureSelectionManager(this);
}
@Override
public StructureSelectionManagerProvider getStructureSelectionManagerProvider()
{
return 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(AlignFrameI alf)
{
return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);
}
/*
* (non-Javadoc)
*
* @see
* jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
* .AlignFrame, java.lang.String)
*/
@Override
public String getSelectedSequencesFrom(AlignFrameI alf, String sep)
{
StringBuffer result = new StringBuffer("");
if (sep == null || sep.length() == 0)
{
sep = separator; // "+0x00AC;
}
if (((AlignFrame) alf).viewport.getSelectionGroup() != null)
{
SequenceI[] seqs = ((AlignFrame) alf).viewport.getSelectionGroup()
.getSequencesInOrder(
((AlignFrame) 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 AlignFrameI 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(
((AlignFrame) alf).viewport.getAlignment().getSequencesArray());
final SequenceI sq = matcher.findIdMatch(sequenceId);
if (sq != null)
{
int apos = -1;
try
{
apos = new Integer(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().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(AlignFrameI 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 AlignFrameI 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 = JalviewAppLoader.separatorListToArray(sequenceIds, sep);
String[] cols = JalviewAppLoader.separatorListToArray(columns, sep);
final SequenceGroup sel = new SequenceGroup();
final ColumnSelection csel = new ColumnSelection();
AlignmentI al = ((AlignFrame) alf).viewport.getAlignment();
jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
((AlignFrame) 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 = new Integer(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 = new Integer(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 = new Integer(cl).intValue();
r--;
} catch (NumberFormatException ex)
{
if (cl.toLowerCase().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()
{
((AlignFrame) alf).select(sel, csel, ((AlignFrame) 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(AlignFrameI alf,
String format, String suffix)
{
try
{
FileFormatI theFormat = FileFormats.getInstance().forName(format);
boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
if (((AlignFrame) 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(((AlignFrame) 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(AlignFrameI alf)
{
return getAlignmentOrderFrom(alf, separator);
}
/*
* (non-Javadoc)
*
* @see
* jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
* , java.lang.String)
*/
@Override
public String getAlignmentOrderFrom(AlignFrameI alf, String sep)
{
AlignmentI alorder = ((AlignFrame) 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(AlignFrameI alf, String order,
String undoName, String sep)
{
String[] ids = JalviewAppLoader.separatorListToArray(order, sep);
SequenceI[] sqs = null;
if (ids != null && ids.length > 0)
{
jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
((AlignFrame) 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 ((AlignFrame) 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(AlignFrameI 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(AlignFrameI alf, String format,
String suffix)
{
try
{
boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
FileFormatI theFormat = FileFormats.getInstance().forName(format);
String reply = new AppletFormatAdapter().formatSequences(theFormat,
((AlignFrame) 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(AlignFrameI alf, String annotation)
{
if (new AnnotationFile().annotateAlignmentView(
((AlignFrame) alf).getAlignViewport(),
annotation, DataSourceType.PASTE))
{
((AlignFrame) alf).alignPanel.fontChanged();
((AlignFrame) alf).alignPanel.setScrollValues(0, 0);
}
else
{
((AlignFrame) 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(AlignFrameI alf, String features,
boolean autoenabledisplay)
{
return ((AlignFrame) 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(AlignFrameI alf, String format)
{
return ((AlignFrame) 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(AlignFrameI alf)
{
return ((AlignFrame) 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(AlignFrameI alf)
{
return ((AlignFrame) alf).newView(null);
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame,
* java.lang.String)
*/
@Override
public AlignFrame newViewFrom(AlignFrameI alf, String name)
{
return ((AlignFrame) 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(AlignFrameI 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, (AlignFrame) af, listener, debug);
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 "
+ ((AlignFrame) 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(AlignFrameI 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, (AlignFrame) af, listener, debug);
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 "
+ ((AlignFrame) 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), debug);
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(AlignFrameI 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.tidyUp();
jsFunctionExec = null;
}
initialAlignFrame = 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(new Integer(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 AlignFrameI alf, final String topRow,
final String leftHandColumn)
{
java.awt.EventQueue.invokeLater(new Runnable()
{
@Override
public void run()
{
try
{
((AlignFrame) alf).scrollTo(new Integer(topRow).intValue(),
new Integer(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 AlignFrameI alf, final String topRow)
{
java.awt.EventQueue.invokeLater(new Runnable()
{
@Override
public void run()
{
try
{
((AlignFrame) alf).scrollToRow(new Integer(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 AlignFrameI alf,
final String leftHandColumn)
{
java.awt.EventQueue.invokeLater(new Runnable()
{
@Override
public void run()
{
try
{
((AlignFrame) alf)
.scrollToColumn(new Integer(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;
boolean checkForJmol = true;
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 JalviewAppLoader appLoader;
public AlignFrame loaderFrame;
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().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"));
}
}
// Background color
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;
}
}
setBackground(new Color(r, g, b));
param = getParameter("label");
if (param != null)
{
launcher.setLabel(param);
}
file = getParameter("file");
if (file == null)
{
file = appLoader.getPastedSequence(this);
}
if (getDefaultParameter("enableSplitFrame", true))
{
file2 = getParameter("file2");
}
embedded = (TRUE.equalsIgnoreCase(getParameter("embedded"))
|| file != null
&& FALSE.equalsIgnoreCase(getParameter("showbutton")));
if (embedded)
{
startLoading();
}
else if (file == null)
{
// jalview initialisation with no alignment. loadAlignment() method can
// still be called to open new alignments.
file = "NO FILE";
fileFound = false;
callInitCallback();
}
else
{
add(launcher);
launcher.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
startLoading();
}
});
}
}
protected void startLoading()
{
LoadingThread loader = new LoadingThread(file, file2, this);
loader.start();
}
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.");
}
}
}
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, debug).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;
public 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)
{
String[] ret = new String[] { path };
protocol = JalviewAppLoader.resolveFileProtocol(applet, ret);
return ret[0];
}
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);
applet.loaderFrame = newAlignFrame;
appLoader.load(applet);
}
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;
}
}
/**
* @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
*/
private boolean jsfallbackEnabled = false;
/**
* parse the string into a list
*
* @param list
* @return elements separated by separator
*/
@Override
public String[] separatorListToArray(String list)
{
return JalviewAppLoader.separatorListToArray(list, separator);
}
/**
* concatenate the list with separator
*
* @param list
* @return concatenated string
*/
@Override
public String arrayToSeparatorList(String[] list)
{
return JalviewAppLoader.arrayToSeparatorList(list, 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(AlignFrameI alf)
{
String lst = arrayToSeparatorList(
((AlignFrame) 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(AlignFrameI alf, boolean visible)
{
return arrayToSeparatorList(
((AlignFrame) alf).getFeatureGroupsOfState(visible));
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui.
* AlignFrame, java.lang.String, boolean)
*/
@Override
public void setFeatureGroupStateOn(final AlignFrameI alf,
final String groups, boolean state)
{
final boolean st = state;// !(state==null || state.equals("") ||
// state.toLowerCase().equals("false"));
java.awt.EventQueue.invokeLater(new Runnable()
{
@Override
public void run()
{
((AlignFrame) 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
*/
@Override
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(AlignFrameI alFrame, String sequenceId,
String pdbEntryString, String pdbFile)
{
return ((AlignFrame) alFrame).addPdbFile(sequenceId, pdbEntryString,
pdbFile);
}
@Override
public 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<>();
@Override
public Hashtable getJSHashes()
{
return jshashes;
}
@Override
public Hashtable> getJSMessages()
{
return jsmessages;
}
private Vector jsExecQueue = new Vector<>();
@Override
public Vector getJsExecQueue(JSFunctionExec exec)
{
jsFunctionExec = exec;
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");
}
/**
* 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 = JalviewAppLoader.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();
}
}
@Override
public AlignViewportI getViewport()
{
return loaderFrame.getAlignViewport();
}
@Override
public void newStructureView(PDBEntry pdb, SequenceI[] seqs,
String[] chains, DataSourceType protocol)
{
loaderFrame.newStructureView(this, pdb, seqs, chains,
protocol);
}
@Override
public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
String[][] chains, String[] protocols)
{
loaderFrame.alignedStructureView(this, pdb, seqs, chains, protocols);
}
@Override
public void updateForAnnotations()
{
loaderFrame.alignPanel.fontChanged();
loaderFrame.alignPanel.setScrollValues(0, 0);
}
@Override
public void setFeatureGroupState(String[] groups, boolean state)
{
loaderFrame.setFeatureGroupState(groups, state);
}
@Override
public boolean parseFeaturesFile(String param, DataSourceType protocol)
{
return loaderFrame.parseFeaturesFile(param, protocol);
}
@Override
public void newFeatureSettings()
{
getViewport().setShowSequenceFeatures(true);
new FeatureSettings(loaderFrame.alignPanel);
}
@Override
public boolean loadScoreFile(String sScoreFile) throws IOException
{
return loaderFrame.loadScoreFile(sScoreFile);
}
@Override
public void loadTree(NewickFile tree, String treeFile) throws IOException
{
loaderFrame.loadTree(tree, treeFile);
}
@Override
public boolean isJsfallbackEnabled()
{
return jsfallbackEnabled;
}
@Override
public JSObject getJSObject()
{
return JSObject.getWindow(this);
}
@Override
public void updateColoursFromMouseOver(Object source,
MouseOverStructureListener listener)
{
}
@Override
public Object[] getSelectionForListener(SequenceGroup seqsel, ColumnSelection colsel,
HiddenColumns hidden, SelectionSource source, Object alignFrame)
{
// System.err.println("Testing selection event relay to
// jsfunction:"+_listener);
String setid = "";
AlignFrame src = (AlignFrame) alignFrame;
if (source != null)
{
if (source instanceof jalview.appletgui.AlignViewport
&& ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame.viewport == source)
{
// should be valid if it just generated an event!
src = ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame;
}
}
String[] seqs = new String[] {};
String[] cols = new String[] {};
int strt = 0, end = (src == null) ? -1
: src.alignPanel.av.getAlignment().getWidth();
if (seqsel != null && seqsel.getSize() > 0)
{
seqs = new String[seqsel.getSize()];
for (int i = 0; i < seqs.length; i++)
{
seqs[i] = seqsel.getSequenceAt(i).getName();
}
if (strt < seqsel.getStartRes())
{
strt = seqsel.getStartRes();
}
if (end == -1 || end > seqsel.getEndRes())
{
end = seqsel.getEndRes();
}
}
if (colsel != null && !colsel.isEmpty())
{
if (end == -1)
{
end = colsel.getMax() + 1;
}
cols = new String[colsel.getSelected().size()];
for (int i = 0; i < cols.length; i++)
{
cols[i] = "" + (1 + colsel.getSelected().get(i).intValue());
}
}
else
{
if (seqsel != null && seqsel.getSize() > 0)
{
// send a valid range, otherwise we send the empty selection
cols = new String[2];
cols[0] = "" + (1 + strt) + "-" + (1 + end);
}
}
return new Object[]
{ src, setid, arrayToSeparatorList(seqs), arrayToSeparatorList(cols) };
}
@Override
public String getJsMessage(String messageclass, String viewId)
{
return JSFunctionExec.getJsMessage(messageclass, viewId, this);
}
@Override
public Object getFrameForSource(VamsasSource source)
{
if (source != null)
{
if (source instanceof jalview.appletgui.AlignViewport
&& ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame.viewport == source)
{
// should be valid if it just generated an event!
return ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame;
}
// TODO: ensure that if '_af' is specified along with a handler
// function, then only events from that alignFrame are sent to that
// function
}
return null;
}
@Override
public FeatureRenderer getNewFeatureRenderer(AlignViewportI vp)
{
return new jalview.appletgui.FeatureRenderer((AlignmentViewport) vp);
}
@Override
public String getSelectedSequencesAsAlignment(String format,
boolean suffix)
{
// TODO Auto-generated method stub
return null;
}
@Override
public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
String format, boolean suffix)
{
// TODO Auto-generated method stub
return null;
}
// /**
// * 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; }
// */
}