/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
-import java.applet.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.util.*;
-
-import jalview.appletgui.*;
-import jalview.datamodel.*;
-import jalview.io.*;
+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 $Revision$
+ * @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 maybe called
+ // The following public methods may be called
// externally, eg via javascript in HTML page
- /**
- * @return String list of selected sequence IDs, each terminated by "¬"
- * (¬)
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences()
*/
+ @Override
public String getSelectedSequences()
{
return getSelectedSequencesFrom(getDefaultTargetFrame());
}
- /**
- * @param sep
- * separator string or null for default
- * @return String list of selected sequence IDs, each terminated by sep or
- * ("¬" as default)
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
*/
+ @Override
public String getSelectedSequences(String sep)
{
return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);
}
- /**
- * @param alf
- * alignframe containing selection
- * @return String list of selected sequence IDs, each terminated by "¬"
+ /*
+ * (non-Javadoc)
*
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
+ * .AlignFrame)
*/
- public String getSelectedSequencesFrom(AlignFrame alf)
+ @Override
+ public String getSelectedSequencesFrom(AlignFrameI alf)
{
- return getSelectedSequencesFrom(alf, "¬");
+ return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);
}
- /**
- * get list of selected sequence IDs separated by given separator
+ /*
+ * (non-Javadoc)
*
- * @param alf
- * window containing selection
- * @param sep
- * separator string to use - default is "¬"
- * @return String list of selected sequence IDs, each terminated by the given
- * separator
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
+ * .AlignFrame, java.lang.String)
*/
- public String getSelectedSequencesFrom(AlignFrame alf, String sep)
+ @Override
+ public String getSelectedSequencesFrom(AlignFrameI alf, String sep)
{
StringBuffer result = new StringBuffer("");
if (sep == null || sep.length() == 0)
{
- sep = "¬";
+ sep = separator; // "+0x00AC;
}
- if (alf.viewport.getSelectionGroup() != null)
+ if (((AlignFrame) alf).viewport.getSelectionGroup() != null)
{
- SequenceI[] seqs = alf.viewport.getSelectionGroup()
- .getSequencesInOrder(alf.viewport.getAlignment());
+ SequenceI[] seqs = ((AlignFrame) alf).viewport.getSelectionGroup()
+ .getSequencesInOrder(
+ ((AlignFrame) alf).viewport.getAlignment());
for (int i = 0; i < seqs.length; i++)
{
return result.toString();
}
- /**
- * get sequences selected in current alignFrame and return their alignment in
- * format 'format' either with or without suffix
+ /*
+ * (non-Javadoc)
*
- * @param alf -
- * where selection is
- * @param format -
- * format of alignment file
- * @param suffix -
- * "true" to append /start-end string to each sequence ID
- * @return selected sequences as flat file or empty string if there was no
- * current selection
+ * @see jalview.bin.JalviewLiteJsApi#highlight(java.lang.String,
+ * java.lang.String, java.lang.String)
*/
- public String getSelectedSequencesAsAlignment(String format, String suffix)
+ @Override
+ public void highlight(String sequenceId, String position,
+ String alignedPosition)
{
- return getSelectedSequencesAsAlignmentFrom(currentAlignFrame, format,
- suffix);
+ highlightIn(getDefaultTargetFrame(), sequenceId, position,
+ alignedPosition);
}
- /**
- * get sequences selected in alf and return their alignment in format 'format'
- * either with or without suffix
+ /*
+ * (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<Integer> 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)
*
- * @param alf -
- * where selection is
- * @param format -
- * format of alignment file
- * @param suffix -
- * "true" to append /start-end string to each sequence ID
- * @return selected sequences as flat file or empty string if there was no
- * current selection
- */
- public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
+ * @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
{
- boolean seqlimits = suffix.equalsIgnoreCase("true");
- if (alf.viewport.getSelectionGroup() != null)
+ FileFormatI theFormat = FileFormats.getInstance().forName(format);
+ boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
+ if (((AlignFrame) alf).viewport.getSelectionGroup() != null)
{
- String reply = new AppletFormatAdapter().formatSequences(format,
- new Alignment(alf.viewport.getSelectionAsNewSequence()),
+ // 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 (Exception ex)
+ } catch (IllegalArgumentException ex)
{
ex.printStackTrace();
- return "Error retrieving alignment in " + format + " format. ";
+ 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");
+ return getAlignmentFrom(getDefaultTargetFrame(), format, TRUE);
}
- public String getAlignmentFrom(AlignFrame alf, String format)
+ /*
+ * (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");
+ 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);
}
- public String getAlignmentFrom(AlignFrame alf, String format,
+ /*
+ * (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");
+ boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
- String reply = new AppletFormatAdapter().formatSequences(format,
- alf.viewport.getAlignment(), seqlimits);
+ FileFormatI theFormat = FileFormats.getInstance().forName(format);
+ String reply = new AppletFormatAdapter().formatSequences(theFormat,
+ ((AlignFrame) alf).viewport.getAlignment(), seqlimits);
return reply;
- } catch (Exception ex)
+ } catch (IllegalArgumentException ex)
{
ex.printStackTrace();
- return "Error retrieving alignment in " + format + " format. ";
+ 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);
}
- public void loadAnnotationFrom(AlignFrame alf, String 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().readAnnotationFile(alf.getAlignViewport()
- .getAlignment(), annotation, AppletFormatAdapter.PASTE))
+ if (new AnnotationFile().annotateAlignmentView(
+ ((AlignFrame) alf).getAlignViewport(),
+ annotation, DataSourceType.PASTE))
{
- alf.alignPanel.fontChanged();
- alf.alignPanel.setScrollValues(0, 0);
+ ((AlignFrame) alf).alignPanel.fontChanged();
+ ((AlignFrame) alf).alignPanel.setScrollValues(0, 0);
}
else
{
- alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
+ ((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);
}
- public String getFeaturesFrom(AlignFrame alf, String format)
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame,
+ * java.lang.String)
+ */
+ @Override
+ public String getFeaturesFrom(AlignFrameI alf, String format)
{
- return alf.outputFeatures(false, format);
+ return ((AlignFrame) alf).outputFeatures(false, format);
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getAnnotation()
+ */
+ @Override
public String getAnnotation()
{
return getAnnotationFrom(getDefaultTargetFrame());
}
- public String getAnnotationFrom(AlignFrame alf)
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame
+ * )
+ */
+ @Override
+ public String getAnnotationFrom(AlignFrameI alf)
{
- return alf.outputAnnotations(false);
+ 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);
}
- public AlignFrame newViewFrom(AlignFrame alf)
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame)
+ */
+ @Override
+ public AlignFrame newViewFrom(AlignFrameI alf)
{
- return alf.newView(null);
+ return ((AlignFrame) alf).newView(null);
}
- public AlignFrame newViewFrom(AlignFrame alf, String name)
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame,
+ * java.lang.String)
+ */
+ @Override
+ public AlignFrame newViewFrom(AlignFrameI alf, String name)
{
- return alf.newView(name);
+ return ((AlignFrame) alf).newView(name);
}
- /**
+ /*
+ * (non-Javadoc)
*
- * @param text
- * alignment file as a string
- * @param title
- * window title
- * @return null or new alignment frame
+ * @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String,
+ * java.lang.String)
*/
+ @Override
public AlignFrame loadAlignment(String text, String title)
{
- Alignment al = null;
- String format = new IdentifyFile().Identify(text,
- AppletFormatAdapter.PASTE);
+ AlignmentI al = null;
+
try
{
- al = new AppletFormatAdapter().readFile(text,
- AppletFormatAdapter.PASTE, format);
+ 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 (java.io.IOException ex)
+ } 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<jalview.javascript.JSFunctionExec> 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();
+ }
+ }
+ });
+
+ }
+
// //////////////////////////////////////////////
// //////////////////////////////////////////////
- static int lastFrameX = 200;
+ public static int lastFrameX = 200;
- static int lastFrameY = 200;
+ public static int lastFrameY = 200;
boolean fileFound = true;
String file = "No file";
- Button launcher = new Button("Start Jalview");
+ String file2 = null;
+
+ Button launcher = new Button(
+ MessageManager.getString("label.start_jalview"));
/**
* The currentAlignFrame is static, it will change if and when the user
* AlignFrame if the applet is started as embedded on the page and then
* afterwards a new view is created.
*/
- public static AlignFrame currentAlignFrame;
+ 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;
+ 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
+ boolean checkForJmol = true;
+
+ boolean checkedForJmol = false; // ensure we don't check for jmol
+
+ // every time the app is re-inited
public boolean jmolAvailable = false;
- public static boolean debug;
+ 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()
{
- /**
- * turn on extra applet debugging
- */
- String dbg = getParameter("debug");
- if (dbg != null)
+ 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)
{
- debug = dbg.toLowerCase().equals("true");
+ useXtrnalSviewer = externalsviewer.trim().toLowerCase().equals(TRUE);
}
/**
* if true disable the check for jmol
String chkforJmol = getParameter("nojmol");
if (chkforJmol != null)
{
- checkForJmol = !chkforJmol.equals("true");
+ checkForJmol = !chkforJmol.equals(TRUE);
}
/**
* get the separator parameter if present
}
else
{
- throw new Error(
- "Invalid separator parameter - must be non-zero length");
+ throw new Error(MessageManager
+ .getString("error.invalid_separator_parameter"));
}
}
+
+ // Background color
+
int r = 255;
int g = 255;
int b = 255;
b = 255;
}
}
+ setBackground(new Color(r, g, b));
param = getParameter("label");
if (param != null)
launcher.setLabel(param);
}
- this.setBackground(new Color(r, g, b));
-
file = getParameter("file");
if (file == null)
{
- // Maybe the sequences are added as parameters
- StringBuffer data = new StringBuffer("PASTE");
- int i = 1;
- while ((file = getParameter("sequence" + i)) != null)
- {
- data.append(file.toString() + "\n");
- i++;
- }
- if (data.length() > 5)
- {
- file = data.toString();
- }
+ file = appLoader.getPastedSequence(this);
}
-
- final JalviewLite applet = this;
- if (getParameter("embedded") != null
- && getParameter("embedded").equalsIgnoreCase("true"))
+ if (getDefaultParameter("enableSplitFrame", true))
{
- // Launch as embedded applet in page
- embedded = true;
- LoadingThread loader = new LoadingThread(file, applet);
- loader.start();
+ file2 = getParameter("file2");
}
- else if (file != null)
+
+ embedded = (TRUE.equalsIgnoreCase(getParameter("embedded"))
+ || file != null
+ && FALSE.equalsIgnoreCase(getParameter("showbutton")));
+ if (embedded)
{
- if (getParameter("showbutton") == null
- || !getParameter("showbutton").equalsIgnoreCase("false"))
- {
- // Add the JalviewLite 'Button' to the page
- add(launcher);
- launcher.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- LoadingThread loader = new LoadingThread(file, applet);
- loader.start();
- }
- });
- }
- else
- {
- // Open jalviewLite immediately.
- LoadingThread loader = new LoadingThread(file, applet);
- loader.start();
- }
+ startLoading();
}
- else
+ 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();
+ }
+ });
}
}
- /**
- * 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
+ 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.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 (currentAlignFrame == frame)
- {
- currentAlignFrame = null;
+ if (vp.applet.currentAlignFrame == frame)
+ {
+ vp.applet.currentAlignFrame = null;
+ }
+ vp.applet = null;
+ vp = null;
+
}
lastFrameX -= 40;
lastFrameY -= 40;
frame.dispose();
}
+ @Override
public void windowActivated(WindowEvent e)
{
if (frame instanceof AlignFrame)
{
- currentAlignFrame = (AlignFrame) frame;
+ ((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame;
if (debug)
{
System.err.println("Activated window " + frame);
/*
* Probably not necessary to do this - see TODO above. (non-Javadoc)
*
- * @see java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent)
+ * @see
+ * java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent
+ * )
*
* public void windowDeactivated(WindowEvent e) { if (currentAlignFrame ==
* frame) { currentAlignFrame = null; if (debug) {
* If file given in parameter not found, displays error message
*
* @param g
- * graphics context
+ * graphics context
*/
+ @Override
public void paint(Graphics g)
{
if (!fileFound)
g.setColor(Color.cyan);
g.fillRect(0, 0, getSize().width, getSize().height);
g.setColor(Color.red);
- g.drawString("Jalview can't open file", 5, 15);
+ g.drawString(
+ 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("Jalview Applet", 50, this.getSize().height / 2 - 30);
- g.drawString("Loading Data...", 50, this.getSize().height / 2);
+ 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;
+ private boolean running = false;
+ @Override
public void run()
{
- if (running || checkedForJmol) {
+ if (running || checkedForJmol)
+ {
return;
}
- running=true;
+ running = true;
if (checkForJmol)
{
try
}
if (!jmolAvailable)
{
- System.out
- .println("Jmol not available - Using MCview for structures");
+ System.out.println(
+ "Jmol not available - Using mc_view for structures");
}
} catch (java.lang.ClassNotFoundException ex)
{
jmolAvailable = false;
if (debug)
{
- System.err
- .println("Skipping Jmol check. Will use MCView (probably)");
+ System.err.println(
+ "Skipping Jmol check. Will use mc_view (probably)");
}
}
- checkedForJmol=true;
- running=false;
+ checkedForJmol = true;
+ running = false;
}
public boolean notFinished()
class LoadingThread extends Thread
{
/**
- * State variable: File source
- */
- String file;
-
- /**
* State variable: protocol for access to file source
*/
- String protocol;
+ DataSourceType protocol;
+
+ String _file; // alignment file or URL spec
+
+ String _file2; // second alignment file or URL spec
- /**
- * State variable: format of file source
- */
- String format;
- String _file;
JalviewLite applet;
- private void dbgMsg(String msg)
+
+ public void dbgMsg(String msg)
{
- if (applet.debug)
+ if (JalviewLite.debug)
{
System.err.println(msg);
}
* update the protocol state variable for accessing the datasource located
* by file.
*
- * @param file
+ * @param path
* @return possibly updated datasource string
*/
- public String setProtocolState(String file)
+ public String resolveFileProtocol(String path)
{
- if (file.startsWith("PASTE"))
- {
- file = file.substring(5);
- protocol = AppletFormatAdapter.PASTE;
- }
- else if (inArchive(file))
- {
- protocol = AppletFormatAdapter.CLASSLOADER;
- }
- else
- {
- file = addProtocol(file);
- protocol = AppletFormatAdapter.URL;
- }
- dbgMsg("Protocol identified as '" + protocol + "'");
- return file;
+
+ String[] ret = new String[] { path };
+ protocol = JalviewAppLoader.resolveFileProtocol(applet, ret);
+ return ret[0];
}
-
- public LoadingThread(String _file, JalviewLite _applet)
+
+ public LoadingThread(String file, String file2, JalviewLite _applet)
{
- this._file=_file;
+ this._file = file;
+ this._file2 = file2;
applet = _applet;
}
+ @Override
public void run()
{
LoadJmolThread jmolchecker = new LoadJmolThread();
while (jmolchecker.notFinished())
{
// wait around until the Jmol check is complete.
- try { Thread.sleep(2); } catch (Exception e) {};
+ 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");
- file = setProtocolState(_file);
+ dbgMsg("Loading thread started with:\n>>file\n" + _file
+ + ">>endfile");
- format = new jalview.io.IdentifyFile().Identify(file, protocol);
- dbgMsg("File identified as '" + format + "'");
dbgMsg("Loading started.");
- Alignment al = null;
- try
- {
- al = new AppletFormatAdapter().readFile(file, protocol, format);
- } catch (java.io.IOException ex)
+
+ AlignFrame newAlignFrame = readAlignment(_file);
+ AlignFrame newAlignFrame2 = readAlignment(_file2);
+ if (newAlignFrame != null)
{
- dbgMsg("File load exception.");
- ex.printStackTrace();
+ addToDisplay(newAlignFrame, newAlignFrame2);
+ applet.loaderFrame = newAlignFrame;
+ appLoader.load(applet);
}
- if ((al != null) && (al.getHeight() > 0))
+ else
{
- dbgMsg("Successfully loaded file.");
- initialAlignFrame = new AlignFrame(al, applet, file, embedded);
- // update the focus.
- currentAlignFrame = initialAlignFrame;
-
- if (protocol == jalview.io.AppletFormatAdapter.PASTE)
- {
- currentAlignFrame.setTitle("Sequences from " + getDocumentBase());
- }
-
- currentAlignFrame.statusBar.setText("Successfully loaded file "
- + file);
-
- String treeFile = applet.getParameter("tree");
- if (treeFile == null)
- {
- treeFile = applet.getParameter("treeFile");
- }
+ fileFound = false;
+ applet.remove(launcher);
+ applet.repaint();
+ callInitCallback();
+ }
+ }
- if (treeFile != null)
+ /**
+ * 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))
{
- try
- {
- treeFile = setProtocolState(treeFile);
- /*
- * if (inArchive(treeFile)) { protocol =
- * AppletFormatAdapter.CLASSLOADER; } else { protocol =
- * AppletFormatAdapter.URL; treeFile = addProtocol(treeFile); }
- */
- jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile,
- protocol);
-
- fin.parse();
-
- if (fin.getTree() != null)
- {
- currentAlignFrame.loadTree(fin, treeFile);
- dbgMsg("Successfuly imported tree.");
- }
- else
- {
- dbgMsg("Tree parameter did not resolve to a valid tree.");
- }
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ al2.alignAs(al1);
+ SplitFrame sf = new SplitFrame(af, af2);
+ sf.addToDisplay(embedded, JalviewLite.this);
+ return;
}
-
- String param = getParameter("features");
- if (param != null)
+ else
{
- param = setProtocolState(param);
-
- currentAlignFrame.parseFeaturesFile(param, protocol);
+ String msg = "Could not map any sequence in " + af2.getTitle()
+ + " as "
+ + (al1.isNucleotide() ? "protein product" : "cDNA")
+ + " for " + af.getTitle();
+ System.err.println(msg);
}
+ }
- param = getParameter("showFeatureSettings");
- if (param != null && param.equalsIgnoreCase("true"))
- {
- currentAlignFrame.viewport.showSequenceFeatures(true);
- new FeatureSettings(currentAlignFrame.alignPanel);
- }
+ af.addToDisplay(embedded);
+ }
- param = getParameter("annotations");
- if (param != null)
+ /**
+ * 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))
{
- param = setProtocolState(param);
-
- if (new AnnotationFile().readAnnotationFile(
- currentAlignFrame.viewport.getAlignment(), param,
- protocol))
+ dbgMsg("Successfully loaded file.");
+ al.setDataset(null);
+ AlignFrame newAlignFrame = new AlignFrame(al, applet,
+ resolvedFile, embedded, false);
+ newAlignFrame.setTitle(resolvedFile);
+ if (initialAlignFrame == null)
{
- currentAlignFrame.alignPanel.fontChanged();
- currentAlignFrame.alignPanel.setScrollValues(0, 0);
+ initialAlignFrame = newAlignFrame;
}
- else
+ // update the focus.
+ currentAlignFrame = newAlignFrame;
+
+ if (protocol == DataSourceType.PASTE)
{
- System.err
- .println("Annotations were not added from annotation file '"
- + param + "'");
+ newAlignFrame.setTitle(MessageManager
+ .formatMessage("label.sequences_from", new Object[]
+ { applet.getDocumentBase().toString() }));
}
- }
+ newAlignFrame.statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_loaded_file", new Object[]
+ { resolvedFile }));
- param = getParameter("jnetfile");
- if (param != null)
- {
- try
- {
- param = setProtocolState(param);
- jalview.io.JPredFile predictions = new jalview.io.JPredFile(
- param, protocol);
- JnetAnnotationMaker.add_annotation(predictions,
- currentAlignFrame.viewport.getAlignment(), 0, false); // false==do
- // not
- // add
- // sequence
- // profile
- // from
- // concise
- // output
- currentAlignFrame.alignPanel.fontChanged();
- currentAlignFrame.alignPanel.setScrollValues(0, 0);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ return newAlignFrame;
}
-
- /*
- * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
- * PDB|1GAQ|1GAQ|C">
- *
- * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
- *
- * <param name="PDBfile3" value="1q0o Q45135_9MICO">
- */
-
- int pdbFileCount = 0;
- do
+ } catch (java.io.IOException ex)
+ {
+ dbgMsg("File load exception.");
+ ex.printStackTrace();
+ if (debug)
{
- if (pdbFileCount > 0)
- param = getParameter("PDBFILE" + pdbFileCount);
- else
- param = getParameter("PDBFILE");
-
- if (param != null)
+ try
{
- PDBEntry pdb = new PDBEntry();
-
- String seqstring;
- SequenceI[] seqs = null;
- String[] chains = null;
-
- StringTokenizer st = new StringTokenizer(param, " ");
-
- if (st.countTokens() < 2)
+ FileParse fp = new FileParse(resolvedFile, protocol);
+ String ln = null;
+ dbgMsg(">>>Dumping contents of '" + resolvedFile + "' " + "("
+ + protocol + ")");
+ while ((ln = fp.nextLine()) != null)
{
- String sequence = applet.getParameter("PDBSEQ");
- if (sequence != null)
- seqs = new SequenceI[]
- { (Sequence) currentAlignFrame.getAlignViewport()
- .getAlignment().findName(sequence) };
-
- }
- else
- {
- param = st.nextToken();
- Vector tmp = new Vector();
- Vector tmp2 = new Vector();
-
- while (st.hasMoreTokens())
- {
- seqstring = st.nextToken();
- StringTokenizer st2 = new StringTokenizer(seqstring, "=");
- if (st2.countTokens() > 1)
- {
- // This is the chain
- tmp2.addElement(st2.nextToken());
- seqstring = st2.nextToken();
- }
- tmp.addElement((Sequence) currentAlignFrame
- .getAlignViewport().getAlignment().findName(
- seqstring));
- }
-
- seqs = new SequenceI[tmp.size()];
- tmp.copyInto(seqs);
- if (tmp2.size() == tmp.size())
- {
- chains = new String[tmp2.size()];
- tmp2.copyInto(chains);
- }
- }
- param = setProtocolState(param);
-
- if (// !jmolAvailable
- // &&
- protocol == AppletFormatAdapter.CLASSLOADER)
- {
- // TODO: verify this Re:
- // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
- // This exception preserves the current behaviour where, even if
- // the local pdb file was identified in the class loader
- protocol = AppletFormatAdapter.URL; // this is probably NOT
- // CORRECT!
- param = addProtocol(param); //
- }
-
- pdb.setFile(param);
-
- if (seqs != null)
- {
- for (int i = 0; i < seqs.length; i++)
- {
- if (seqs[i] != null)
- {
- ((Sequence) seqs[i]).addPDBId(pdb);
- }
- else
- {
- if (JalviewLite.debug)
- {
- // this may not really be a problem but we give a warning
- // anyway
- System.err
- .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
- + i + ")");
- }
- }
- }
-
- if (jmolAvailable)
- {
- new jalview.appletgui.AppletJmol(pdb, seqs, chains,
- currentAlignFrame.alignPanel, protocol);
- lastFrameX += 40;
- lastFrameY += 40;
- }
- else
- new MCview.AppletPDBViewer(pdb, seqs, chains,
- currentAlignFrame.alignPanel, protocol);
+ dbgMsg(ln);
}
+ dbgMsg(">>>Dump finished.");
+ } catch (Exception e)
+ {
+ System.err.println(
+ "Exception when trying to dump the content of the file parameter.");
+ e.printStackTrace();
}
-
- pdbFileCount++;
- } while (pdbFileCount < 10);
-
- // ///////////////////////////
- // modify display of features
- //
- // hide specific groups
- param = getParameter("hidefeaturegroups");
- if (param != null)
- {
- applet.setFeatureGroupState(param, false);
}
- // show specific groups
- param = getParameter("showfeaturegroups");
- if (param != null)
- {
- applet.setFeatureGroupState(param, true);
- }
- }
- else
- {
- fileFound = false;
- remove(launcher);
- repaint();
- }
- }
-
- /**
- * Discovers whether the given file is in the Applet Archive
- *
- * @param file
- * String
- * @return boolean
- */
- boolean inArchive(String file)
- {
- // This might throw a security exception in certain browsers
- // Netscape Communicator for instance.
- try
- {
- boolean rtn = (getClass().getResourceAsStream("/" + file) != null);
- if (debug)
- {
- System.err.println("Resource '" + file + "' was "
- + (rtn ? "" : "not") + " located by classloader.");
- }
- return rtn;
- } catch (Exception ex)
- {
- System.out.println("Exception checking resources: " + file + " "
- + ex);
- return false;
}
+ return null;
}
- String addProtocol(String file)
- {
- if (file.indexOf("://") == -1)
- {
- file = getCodeBase() + file;
- if (debug)
- {
- System.err.println("Prepended codebase for resource: '" + file
- + "'");
- }
- }
-
- return file;
- }
}
/**
* return null with an error message on System.err indicating the
* fact.
*/
- protected AlignFrame getDefaultTargetFrame()
+ public AlignFrame getDefaultTargetFrame()
{
if (currentAlignFrame != null)
{
{
return initialAlignFrame;
}
- System.err
- .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
+ System.err.println(
+ "Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
return null;
}
/**
* separator used for separatorList
*/
- protected String separator = "|"; // this is a safe(ish) separator - tabs
+ protected String separator = "" + ((char) 0x00AC); // the default used to be
+ // '|' but many sequence
+ // IDS include pipes.
- // don't work for firefox
+ /**
+ * 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)
{
- int seplen = separator.length();
- if (list == null || list.equals(""))
- return null;
- java.util.Vector jv = new Vector();
- int cp = 0, pos;
- while ((pos = list.indexOf(separator, cp)) > cp)
- {
- jv.addElement(list.substring(cp, pos));
- cp = pos + seplen;
- }
- if (cp < list.length())
- {
- jv.addElement(list.substring(cp));
- }
- if (jv.size() > 0)
- {
- String[] v = new String[jv.size()];
- for (int i = 0; i < v.length; i++)
- {
- v[i] = (String) jv.elementAt(i);
- }
- jv.removeAllElements();
- if (debug)
- {
- System.err.println("Array from '" + separator
- + "' separated List:\n" + v.length);
- for (int i = 0; i < v.length; i++)
- {
- System.err.println("item " + i + " '" + v[i] + "'");
- }
- }
- return v;
- }
- if (debug)
- {
- System.err.println("Empty Array from '" + separator
- + "' separated List");
- }
- return null;
+ return JalviewAppLoader.separatorListToArray(list, separator);
}
/**
* @param list
* @return concatenated string
*/
+ @Override
public String arrayToSeparatorList(String[] list)
{
- StringBuffer v = new StringBuffer();
- if (list != null)
- {
- for (int i = 0, iSize = list.length - 1; i < iSize; i++)
- {
- if (list[i] != null)
- {
- v.append(list[i]);
- }
- v.append(separator);
- }
- if (list[list.length - 1] != null)
- {
- v.append(list[list.length - 1]);
- }
- if (debug)
- {
- System.err.println("Returning '" + separator
- + "' separated List:\n");
- System.err.println(v);
- }
- return v.toString();
- }
- if (debug)
- {
- System.err.println("Returning empty '" + separator
- + "' separated List\n");
- }
- return "";
+ return JalviewAppLoader.arrayToSeparatorList(list, separator);
}
- /**
- * @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroups()
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
*/
+ @Override
public String getFeatureGroups()
{
- String lst = arrayToSeparatorList(getDefaultTargetFrame()
- .getFeatureGroups());
+ String lst = arrayToSeparatorList(
+ getDefaultTargetFrame().getFeatureGroups());
return lst;
}
- /**
- * @param alf
- * alignframe to get feature groups on
- * @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroups()
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame
+ * )
*/
- public String getFeatureGroupsOn(AlignFrame alf)
+ @Override
+ public String getFeatureGroupsOn(AlignFrameI alf)
{
- String lst = arrayToSeparatorList(alf.getFeatureGroups());
+ String lst = arrayToSeparatorList(
+ ((AlignFrame) alf).getFeatureGroups());
return lst;
}
- /**
- * @param visible
- * @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)
*/
+ @Override
public String getFeatureGroupsOfState(boolean visible)
{
- return arrayToSeparatorList(getDefaultTargetFrame()
- .getFeatureGroupsOfState(visible));
+ return arrayToSeparatorList(
+ getDefaultTargetFrame().getFeatureGroupsOfState(visible));
}
- /**
- * @param alf
- * align frame to get groups of state visible
- * @param visible
- * @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui
+ * .AlignFrame, boolean)
*/
- public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
+ @Override
+ public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible)
{
- return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
+ return arrayToSeparatorList(
+ ((AlignFrame) alf).getFeatureGroupsOfState(visible));
}
- /**
- * @param groups
- * tab separated list of group names
- * @param state
- * true or false
- * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[],
- * boolean)
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui.
+ * AlignFrame, java.lang.String, boolean)
*/
- public void setFeatureGroupStateOn(AlignFrame alf, String groups,
- boolean state)
+ @Override
+ public void setFeatureGroupStateOn(final AlignFrameI alf,
+ final String groups, boolean state)
{
- boolean st = state;// !(state==null || state.equals("") ||
+ final boolean st = state;// !(state==null || state.equals("") ||
// state.toLowerCase().equals("false"));
- alf.setFeatureGroupState(separatorListToArray(groups), st);
+ 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);
}
- /**
- * List separator string
+ /*
+ * (non-Javadoc)
*
- * @return the separator
+ * @see jalview.bin.JalviewLiteJsApi#getSeparator()
*/
+ @Override
public String getSeparator()
{
return separator;
}
- /**
- * List separator string
+ /*
+ * (non-Javadoc)
*
- * @param separator
- * the separator to set
+ * @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<String, int[]> jshashes = new Hashtable<>();
+
+ private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<>();
+
+
+ @Override
+ public Hashtable<String, int[]> getJSHashes()
+ {
+ return jshashes;
}
+
+ @Override
+ public Hashtable<String, Hashtable<String, String[]>> getJSMessages()
+ {
+ return jsmessages;
+ }
+
+ private Vector<Runnable> jsExecQueue = new Vector<>();
+
+ @Override
+ public Vector<Runnable> 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; }
+ // */
}
git://source.jalview.org / jalview.git / blobdiff