/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.
- *
+ * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
+import jalview.analysis.AlignmentUtils;
+import jalview.api.StructureSelectionManagerProvider;
import jalview.appletgui.AlignFrame;
+import jalview.appletgui.AlignViewport;
import jalview.appletgui.EmbmenuFrame;
import jalview.appletgui.FeatureSettings;
+import jalview.appletgui.SplitFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileParse;
import jalview.io.IdentifyFile;
+import jalview.io.JPredFile;
import jalview.io.JnetAnnotationMaker;
+import jalview.io.NewickFile;
+import jalview.javascript.JSFunctionExec;
+import jalview.javascript.JalviewLiteJsApi;
import jalview.javascript.JsCallBack;
+import jalview.javascript.MouseOverStructureListener;
import jalview.structure.SelectionListener;
import jalview.structure.StructureSelectionManager;
+import jalview.util.HttpUtils;
+import jalview.util.MessageManager;
import java.applet.Applet;
import java.awt.Button;
import java.awt.Color;
import java.awt.Component;
+import java.awt.EventQueue;
import java.awt.Font;
import java.awt.Frame;
import java.awt.Graphics;
import java.awt.event.WindowEvent;
import java.io.BufferedReader;
import java.io.InputStreamReader;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
import java.util.StringTokenizer;
import java.util.Vector;
+import netscape.javascript.JSObject;
+
/**
* Jalview Applet. Runs in Java 1.18 runtime
*
* @author $author$
- * @version $Revision$
+ * @version $Revision: 1.92 $
*/
-public class JalviewLite extends Applet
+public class JalviewLite extends Applet implements
+ StructureSelectionManagerProvider, JalviewLiteJsApi
{
+ private static final String TRUE = "true";
+
+ private static final String FALSE = "false";
+
+ public StructureSelectionManager getStructureSelectionManager()
+ {
+ return StructureSelectionManager.getStructureSelectionManager(this);
+ }
+
// /////////////////////////////////////////
- // The following public methods 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)
*/
+ @Override
public String getSelectedSequencesFrom(AlignFrame 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)
*/
+ @Override
public String getSelectedSequencesFrom(AlignFrame alf, String sep)
{
StringBuffer result = new StringBuffer("");
if (sep == null || sep.length() == 0)
{
- sep = "¬";
+ sep = separator; // "+0x00AC;
}
if (alf.viewport.getSelectionGroup() != null)
{
return result.toString();
}
- /**
+ /*
+ * (non-Javadoc)
*
- * @param sequenceId id of sequence to highlight
- * @param position integer position [ tobe implemented or range ] on sequence
- * @param alignedPosition true/false/empty string - indicate if position is an alignment column or unaligned sequence position
+ * @see jalview.bin.JalviewLiteJsApi#highlight(java.lang.String,
+ * java.lang.String, java.lang.String)
*/
- public void highlight(String sequenceId, String position, String alignedPosition)
+ @Override
+ public void highlight(String sequenceId, String position,
+ String alignedPosition)
{
- highlight(currentAlignFrame, sequenceId, position, alignedPosition);
+ highlightIn(getDefaultTargetFrame(), sequenceId, position,
+ alignedPosition);
}
- /**
+
+ /*
+ * (non-Javadoc)
*
- * @param sequenceId id of sequence to highlight
- * @param position integer position [ tobe implemented or range ] on sequence
- * @param alignedPosition false, blank or something else - indicate if position is an alignment column or unaligned sequence position
+ * @see jalview.bin.JalviewLiteJsApi#highlightIn(jalview.appletgui.AlignFrame,
+ * java.lang.String, java.lang.String, java.lang.String)
*/
- public void highlight(AlignFrame alf, String sequenceId, String position, String alignedPosition)
+ @Override
+ public void highlightIn(final AlignFrame alf, final String sequenceId,
+ final String position, final String alignedPosition)
{
- SequenceI sq = alf.getAlignViewport().getAlignment().findName(sequenceId);
- if (sq!=null)
+ // TODO: could try to highlight in all alignments if alf==null
+ jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+ alf.viewport.getAlignment().getSequencesArray());
+ final SequenceI sq = matcher.findIdMatch(sequenceId);
+ if (sq != null)
{
- int pos, apos=-1;
- try {
+ 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))
+ 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
{
- StructureSelectionManager.getStructureSelectionManager().mouseOverVamsasSequence(sq,sq.findIndex(apos));
- } else {
- StructureSelectionManager.getStructureSelectionManager().mouseOverVamsasSequence(sq,apos);
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ StructureSelectionManager.getStructureSelectionManager(me)
+ .mouseOverVamsasSequence(sq, pos, null);
+ }
+ });
}
-
}
}
- /**
- * select regions of the currrent alignment frame
+
+ /*
+ * (non-Javadoc)
*
- * @param sequenceIds String separated list of sequence ids or empty string
- * @param columns
- * String separated list { column range or column, ..} or empty string
+ * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
+ * java.lang.String)
*/
+ @Override
public void select(String sequenceIds, String columns)
{
- select(currentAlignFrame, sequenceIds, columns, "¬");
+ selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator);
}
- /**
- * select regions of the currrent alignment frame
+ /*
+ * (non-Javadoc)
*
- * @param toselect
- * String separated list { column range, seq1...seqn sequence ids }
- * @param sep
- * separator between toselect fields
+ * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
+ * java.lang.String, java.lang.String)
*/
+ @Override
public void select(String sequenceIds, String columns, String sep)
{
- select(currentAlignFrame, sequenceIds, columns, sep);
+ selectIn(getDefaultTargetFrame(), sequenceIds, columns, sep);
}
- /**
- * select regions of the given alignment frame
+ /*
+ * (non-Javadoc)
*
- * @param alf
- * @param toselect
- * String separated list { column range, seq1...seqn sequence ids }
- * @param sep
- * separator between toselect fields
+ * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
+ * java.lang.String, java.lang.String)
*/
- public void select(AlignFrame alf, String sequenceIds, String columns)
+ @Override
+ public void selectIn(AlignFrame alf, String sequenceIds, String columns)
{
- select(alf, sequenceIds, columns, separator);
+ selectIn(alf, sequenceIds, columns, separator);
}
- /**
- * select regions of the given alignment frame
+ /*
+ * (non-Javadoc)
*
- * @param alf
- * @param toselect
- * String separated list { column range, seq1...seqn sequence ids }
- * @param sep
- * separator between toselect fields
+ * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
+ * java.lang.String, java.lang.String, java.lang.String)
*/
- public void select(AlignFrame alf, String sequenceIds, String columns,
- String sep)
+ @Override
+ public void selectIn(final AlignFrame alf, String sequenceIds,
+ String columns, String sep)
{
if (sep == null || sep.length() == 0)
{
sep = separator;
}
+ else
+ {
+ if (debug)
+ {
+ System.err.println("Selecting region using separator string '"
+ + separator + "'");
+ }
+ }
// deparse fields
String[] ids = separatorListToArray(sequenceIds, sep);
String[] cols = separatorListToArray(columns, sep);
- SequenceGroup sel = new SequenceGroup();
- ColumnSelection csel = new ColumnSelection();
+ final SequenceGroup sel = new SequenceGroup();
+ final ColumnSelection csel = new ColumnSelection();
AlignmentI al = alf.viewport.getAlignment();
+ jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+ alf.viewport.getAlignment().getSequencesArray());
int start = 0, end = al.getWidth(), alw = al.getWidth();
+ boolean seqsfound = true;
if (ids != null && ids.length > 0)
{
+ seqsfound = false;
for (int i = 0; i < ids.length; i++)
{
if (ids[i].trim().length() == 0)
{
continue;
}
- SequenceI sq = al.findName(ids[i]);
+ 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;
r--;
} catch (NumberFormatException ex)
{
- System.err
- .println("ERROR: Couldn't parse integer from point selection element of column selection string '"
- + cl + "'");
- return;
+ 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)
{
}
}
}
- sel.setStartRes(start);
- sel.setEndRes(end);
- alf.select(sel, csel);
-
+ 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<Integer>(csel.getSelected());
+ csel.clear();
+ for (Integer selectedCol : cs)
+ {
+ csel.addElement(rs.findIndex(selectedCol));
+ }
+ }
+ sel.setStartRes(start);
+ sel.setEndRes(end);
+ EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ alf.select(sel, csel);
+ }
+ });
+ }
}
- /**
- * get sequences selected in current alignFrame and return their alignment in
- * format 'format' either with or without suffix
- *
- * @param alf
- * - where selection is
- * @param format
- * - format of alignment file
- * @param suffix
- * - "true" to append /start-end string to each sequence ID
- * @return selected sequences as flat file or empty string if there was no
- * current selection
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignment(java.lang.
+ * String, java.lang.String)
*/
+ @Override
public String getSelectedSequencesAsAlignment(String format, String suffix)
{
- return getSelectedSequencesAsAlignmentFrom(currentAlignFrame, format,
- suffix);
+ return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(),
+ format, suffix);
}
- /**
- * get sequences selected in alf and return their alignment in format 'format'
- * either with or without suffix
- *
- * @param alf
- * - where selection is
- * @param format
- * - format of alignment file
- * @param suffix
- * - "true" to append /start-end string to each sequence ID
- * @return selected sequences as flat file or empty string if there was no
- * current selection
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignmentFrom(jalview
+ * .appletgui.AlignFrame, java.lang.String, java.lang.String)
*/
+ @Override
public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
String format, String suffix)
{
try
{
- boolean seqlimits = suffix.equalsIgnoreCase("true");
+ boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
if (alf.viewport.getSelectionGroup() != null)
{
+ // JBPNote: getSelectionAsNewSequence behaviour has changed - this
+ // method now returns a full copy of sequence data
+ // TODO consider using getSequenceSelection instead here
String reply = new AppletFormatAdapter().formatSequences(format,
new Alignment(alf.viewport.getSelectionAsNewSequence()),
seqlimits);
return "";
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder()
+ */
+ @Override
+ public String getAlignmentOrder()
+ {
+ return getAlignmentOrderFrom(getDefaultTargetFrame());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
+ * )
+ */
+ @Override
+ public String getAlignmentOrderFrom(AlignFrame alf)
+ {
+ return getAlignmentOrderFrom(alf, separator);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
+ * , java.lang.String)
+ */
+ @Override
+ public String getAlignmentOrderFrom(AlignFrame alf, String sep)
+ {
+ AlignmentI alorder = alf.getAlignViewport().getAlignment();
+ String[] order = new String[alorder.getHeight()];
+ for (int i = 0; i < order.length; i++)
+ {
+ order[i] = alorder.getSequenceAt(i).getName();
+ }
+ return arrayToSeparatorList(order);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
+ * java.lang.String)
+ */
+ @Override
+ public String orderBy(String order, String undoName)
+ {
+ return orderBy(order, undoName, separator);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
+ * java.lang.String, java.lang.String)
+ */
+ @Override
+ public String orderBy(String order, String undoName, String sep)
+ {
+ return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#orderAlignmentBy(jalview.appletgui.AlignFrame,
+ * java.lang.String, java.lang.String, java.lang.String)
+ */
+ @Override
+ public String orderAlignmentBy(AlignFrame alf, String order,
+ String undoName, String sep)
+ {
+ String[] ids = separatorListToArray(order, sep);
+ SequenceI[] sqs = null;
+ if (ids != null && ids.length > 0)
+ {
+ jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+ alf.viewport.getAlignment().getSequencesArray());
+ int s = 0;
+ sqs = new SequenceI[ids.length];
+ for (int i = 0; i < ids.length; i++)
+ {
+ if (ids[i].trim().length() == 0)
+ {
+ continue;
+ }
+ SequenceI sq = matcher.findIdMatch(ids[i]);
+ if (sq != null)
+ {
+ sqs[s++] = sq;
+ }
+ }
+ if (s > 0)
+ {
+ SequenceI[] sqq = new SequenceI[s];
+ System.arraycopy(sqs, 0, sqq, 0, s);
+ sqs = sqq;
+ }
+ else
+ {
+ sqs = null;
+ }
+ }
+ if (sqs == null)
+ {
+ return "";
+ }
+ ;
+ final AlignmentOrder aorder = new AlignmentOrder(sqs);
+
+ if (undoName != null && undoName.trim().length() == 0)
+ {
+ undoName = null;
+ }
+ final String _undoName = undoName;
+ // TODO: deal with synchronization here: cannot raise any events until after
+ // this has returned.
+ return alf.sortBy(aorder, _undoName) ? TRUE : "";
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String)
+ */
+ @Override
public String getAlignment(String format)
{
- return getAlignmentFrom(getDefaultTargetFrame(), format, "true");
+ return getAlignmentFrom(getDefaultTargetFrame(), format, TRUE);
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
+ * java.lang.String)
+ */
+ @Override
public String getAlignmentFrom(AlignFrame alf, String format)
{
- return getAlignmentFrom(alf, format, "true");
+ return getAlignmentFrom(alf, format, TRUE);
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String,
+ * java.lang.String)
+ */
+ @Override
public String getAlignment(String format, String suffix)
{
return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
+ * java.lang.String, java.lang.String)
+ */
+ @Override
public String getAlignmentFrom(AlignFrame alf, String format,
String suffix)
{
try
{
- boolean seqlimits = suffix.equalsIgnoreCase("true");
+ boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
String reply = new AppletFormatAdapter().formatSequences(format,
alf.viewport.getAlignment(), seqlimits);
}
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
+ */
+ @Override
public void loadAnnotation(String annotation)
{
loadAnnotationFrom(getDefaultTargetFrame(), annotation);
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
+ * , java.lang.String)
+ */
+ @Override
public void loadAnnotationFrom(AlignFrame alf, String annotation)
{
- if (new AnnotationFile().readAnnotationFile(alf.getAlignViewport()
- .getAlignment(), annotation, AppletFormatAdapter.PASTE))
+ if (new AnnotationFile().annotateAlignmentView(alf.getAlignViewport(),
+ annotation, AppletFormatAdapter.PASTE))
{
alf.alignPanel.fontChanged();
alf.alignPanel.setScrollValues(0, 0);
}
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
+ */
+ @Override
+ public void loadFeatures(String features, boolean autoenabledisplay)
+ {
+ loadFeaturesFrom(getDefaultTargetFrame(), features, autoenabledisplay);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
+ * , java.lang.String)
+ */
+ @Override
+ public boolean loadFeaturesFrom(AlignFrame alf, String features,
+ boolean autoenabledisplay)
+ {
+ return alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE,
+ autoenabledisplay);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String)
+ */
+ @Override
public String getFeatures(String format)
{
return getFeaturesFrom(getDefaultTargetFrame(), format);
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame,
+ * java.lang.String)
+ */
+ @Override
public String getFeaturesFrom(AlignFrame alf, String format)
{
return alf.outputFeatures(false, format);
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getAnnotation()
+ */
+ @Override
public String getAnnotation()
{
return getAnnotationFrom(getDefaultTargetFrame());
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame
+ * )
+ */
+ @Override
public String getAnnotationFrom(AlignFrame alf)
{
return alf.outputAnnotations(false);
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#newView()
+ */
+ @Override
public AlignFrame newView()
{
return newViewFrom(getDefaultTargetFrame());
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String)
+ */
+ @Override
public AlignFrame newView(String name)
{
return newViewFrom(getDefaultTargetFrame(), name);
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame)
+ */
+ @Override
public AlignFrame newViewFrom(AlignFrame alf)
{
return alf.newView(null);
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame,
+ * java.lang.String)
+ */
+ @Override
public AlignFrame newViewFrom(AlignFrame alf, String name)
{
return alf.newView(name);
}
- /**
+ /*
+ * (non-Javadoc)
*
- * @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;
+ AlignmentI al = null;
- String format = new IdentifyFile().Identify(text,
+ String format = new IdentifyFile().identify(text,
AppletFormatAdapter.PASTE);
try
{
return null;
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String)
+ */
+ @Override
public void setMouseoverListener(String listener)
{
setMouseoverListener(currentAlignFrame, listener);
}
- private Vector mouseoverListeners = new Vector();
+ private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<jalview.javascript.JSFunctionExec>();
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame
+ * , java.lang.String)
+ */
+ @Override
public void setMouseoverListener(AlignFrame af, String listener)
{
if (listener != null)
}
jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener(
this, af, listener);
- mouseoverListeners.addElement(mol);
- StructureSelectionManager.getStructureSelectionManager()
+ javascriptListeners.addElement(mol);
+ StructureSelectionManager.getStructureSelectionManager(this)
.addStructureViewerListener(mol);
if (debug)
{
System.err.println("Added a mouseover listener for "
+ ((af == null) ? "All frames" : "Just views for "
+ af.getAlignViewport().getSequenceSetId()));
- System.err.println("There are now " + mouseoverListeners.size()
+ 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(currentAlignFrame, listener);
+ setSelectionListener(null, listener);
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame
+ * , java.lang.String)
+ */
+ @Override
public void setSelectionListener(AlignFrame af, String listener)
{
if (listener != null)
}
jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender(
this, af, listener);
- mouseoverListeners.addElement(mol);
- StructureSelectionManager.getStructureSelectionManager()
+ javascriptListeners.addElement(mol);
+ StructureSelectionManager.getStructureSelectionManager(this)
.addSelectionListener(mol);
if (debug)
{
System.err.println("Added a selection listener for "
+ ((af == null) ? "All frames" : "Just views for "
+ af.getAlignViewport().getSequenceSetId()));
- System.err.println("There are now " + mouseoverListeners.size()
+ System.err.println("There are now " + javascriptListeners.size()
+ " listeners in total.");
}
}
/**
- * remove any callback using the given listener function and associated with
- * the given alignFrame (or null for all callbacks)
- *
- * @param af
- * (may be null)
+ * Callable from javascript to register a javascript function to pass events
+ * to a structure viewer.
+ *
* @param listener
- * (may be null)
+ * the name of a javascript function
+ * @param modelSet
+ * a token separated list of PDB file names listened for
+ * @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String,
+ * java.lang.String)
+ */
+ @Override
+ public void setStructureListener(String listener, String modelSet)
+ {
+ if (listener != null)
+ {
+ listener = listener.trim();
+ if (listener.length() == 0)
+ {
+ System.err
+ .println("jalview Javascript error: Ignoring empty function for selection listener.");
+ return;
+ }
+ }
+ MouseOverStructureListener mol = new MouseOverStructureListener(this,
+ listener, separatorListToArray(modelSet));
+ javascriptListeners.addElement(mol);
+ StructureSelectionManager.getStructureSelectionManager(this)
+ .addStructureViewerListener(mol);
+ if (debug)
+ {
+ System.err.println("Added a javascript structure viewer listener '"
+ + listener + "'");
+ System.err.println("There are now " + javascriptListeners.size()
+ + " listeners in total.");
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui
+ * .AlignFrame, java.lang.String)
*/
+ @Override
public void removeJavascriptListener(AlignFrame af, String listener)
{
if (listener != null)
}
}
boolean rprt = false;
- for (int ms=0,msSize=mouseoverListeners.size();ms<msSize;)
+ for (int ms = 0, msSize = javascriptListeners.size(); ms < msSize;)
{
- Object lstn = mouseoverListeners.elementAt(ms);
+ Object lstn = javascriptListeners.elementAt(ms);
JsCallBack lstner = (JsCallBack) lstn;
if ((af == null || lstner.getAlignFrame() == af)
&& (listener == null || lstner.getListenerFunction().equals(
listener)))
{
- mouseoverListeners.removeElement(lstner);
+ javascriptListeners.removeElement(lstner);
msSize--;
if (lstner instanceof SelectionListener)
{
- StructureSelectionManager.getStructureSelectionManager()
+ StructureSelectionManager.getStructureSelectionManager(this)
.removeSelectionListener((SelectionListener) lstner);
}
else
{
- StructureSelectionManager.getStructureSelectionManager()
+ StructureSelectionManager.getStructureSelectionManager(this)
.removeStructureViewerListener(lstner, null);
}
rprt = debug;
{
System.err.println("Removed listener '" + listener + "'");
}
- } else {
+ }
+ else
+ {
ms++;
}
}
if (rprt)
{
- System.err.println("There are now " + mouseoverListeners.size()
+ System.err.println("There are now " + javascriptListeners.size()
+ " listeners in total.");
}
}
+ @Override
public void stop()
{
- if (mouseoverListeners!=null)
+ 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 (mouseoverListeners.size()>0)
+ while (javascriptListeners.size() > 0)
{
- Object mol = mouseoverListeners.elementAt(0);
- mouseoverListeners.removeElement(mol);
+ jalview.javascript.JSFunctionExec mol = javascriptListeners
+ .elementAt(0);
+ javascriptListeners.removeElement(mol);
if (mol instanceof SelectionListener)
{
- StructureSelectionManager.getStructureSelectionManager().removeSelectionListener((SelectionListener)mol);
- } else {
- StructureSelectionManager.getStructureSelectionManager().removeStructureViewerListener(mol, null);
+ StructureSelectionManager.getStructureSelectionManager(this)
+ .removeSelectionListener((SelectionListener) mol);
}
+ else
+ {
+ StructureSelectionManager.getStructureSelectionManager(this)
+ .removeStructureViewerListener(mol, null);
+ }
+ mol.jvlite = null;
}
}
+ if (jsFunctionExec != null)
+ {
+ jsFunctionExec.stopQueue();
+ jsFunctionExec.jvlite = null;
+ }
+ initialAlignFrame = null;
+ jsFunctionExec = null;
+ javascriptListeners = null;
+ StructureSelectionManager.release(this);
}
- /**
- * send a mouseover message to all the alignment windows associated with the
- * given residue in the pdbfile
+
+ private jalview.javascript.JSFunctionExec jsFunctionExec;
+
+ /*
+ * (non-Javadoc)
*
- * @param pdbResNum
- * @param chain
- * @param pdbfile
+ * @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String,
+ * java.lang.String, java.lang.String)
*/
- public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
+ @Override
+ public void mouseOverStructure(final String pdbResNum,
+ final String chain, final String pdbfile)
{
- StructureSelectionManager.getStructureSelectionManager()
- .mouseOverStructure(pdbResNum, chain, 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 AlignFrame alf, final String topRow,
+ final String leftHandColumn)
+ {
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ try
+ {
+ alf.scrollTo(new Integer(topRow).intValue(), new Integer(
+ leftHandColumn).intValue());
- public static int lastFrameX = 200;
+ } catch (Exception ex)
+ {
+ System.err.println("Couldn't parse integer arguments (topRow='"
+ + topRow + "' and leftHandColumn='" + leftHandColumn
+ + "')");
+ ex.printStackTrace();
+ }
+ }
+ });
+ }
- public static int lastFrameY = 200;
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.javascript.JalviewLiteJsApi#scrollViewToRowIn(jalview.appletgui
+ * .AlignFrame, java.lang.String)
+ */
+ @Override
+ public void scrollViewToRowIn(final AlignFrame alf, final String topRow)
+ {
- boolean fileFound = true;
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ try
+ {
+ alf.scrollToRow(new Integer(topRow).intValue());
- String file = "No file";
+ } catch (Exception ex)
+ {
+ System.err.println("Couldn't parse integer arguments (topRow='"
+ + topRow + "')");
+ ex.printStackTrace();
+ }
- Button launcher = new Button("Start Jalview");
+ }
+ });
+ }
- /**
- * The currentAlignFrame is static, it will change if and when the user
- * selects a new window. Note that it will *never* point back to the embedded
- * AlignFrame if the applet is started as embedded on the page and then
- * afterwards a new view is created.
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.javascript.JalviewLiteJsApi#scrollViewToColumnIn(jalview.appletgui
+ * .AlignFrame, java.lang.String)
*/
- public static AlignFrame currentAlignFrame = null;
+ @Override
+ public void scrollViewToColumnIn(final AlignFrame alf,
+ final String leftHandColumn)
+ {
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ try
+ {
+ 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
private boolean alignPdbStructures = false;
+ /**
+ * use an external structure viewer exclusively (no jmols or MCViews will be
+ * opened by JalviewLite itself)
+ */
+ public boolean useXtrnalSviewer = false;
+
public static boolean debug = false;
- static String builddate = null, version = null;
+ static String builddate = null, version = null, installation = null;
private static void initBuildDetails()
{
{
builddate = "unknown";
version = "test";
+ installation = "applet";
java.net.URL url = JalviewLite.class
.getResource("/.build_properties");
if (url != null)
{
builddate = line.substring(line.indexOf("=") + 1);
}
+ if (line.indexOf("INSTALLATION") > -1)
+ {
+ installation = line.substring(line.indexOf("=") + 1);
+ }
}
} catch (Exception ex)
{
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()
{
- // remove any handlers that might be hanging around from an earlier instance
-
- /**
- * 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)
{
- debug = dbg.toLowerCase().equals("true");
+ 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");
+ checkForJmol = !chkforJmol.equals(TRUE);
}
/**
* get the separator parameter if present
else
{
throw new Error(
- "Invalid separator parameter - must be non-zero length");
+ MessageManager
+ .getString("error.invalid_separator_parameter"));
}
}
int r = 255;
b = 255;
}
}
-
param = getParameter("label");
if (param != null)
{
launcher.setLabel(param);
}
- this.setBackground(new Color(r, g, b));
+ setBackground(new Color(r, g, b));
file = getParameter("file");
file = data.toString();
}
}
+ if (getDefaultParameter("enableSplitFrame", true))
+ {
+ file2 = getParameter("file2");
+ }
- final JalviewLite applet = this;
- if (getParameter("embedded") != null
- && getParameter("embedded").equalsIgnoreCase("true"))
+ embedded = TRUE.equalsIgnoreCase(getParameter("embedded"));
+ if (embedded)
{
- // Launch as embedded applet in page
- embedded = true;
- LoadingThread loader = new LoadingThread(file, applet);
+ LoadingThread loader = new LoadingThread(file, file2, this);
loader.start();
}
else if (file != null)
{
- if (getParameter("showbutton") == null
- || !getParameter("showbutton").equalsIgnoreCase("false"))
+ /*
+ * Start the applet immediately or show a button to start it
+ */
+ if (FALSE.equalsIgnoreCase(getParameter("showbutton")))
+ {
+ LoadingThread loader = new LoadingThread(file, file2, this);
+ loader.start();
+ }
+ else
{
- // Add the JalviewLite 'Button' to the page
add(launcher);
launcher.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- LoadingThread loader = new LoadingThread(file, applet);
+ LoadingThread loader = new LoadingThread(file, file2,
+ JalviewLite.this);
loader.start();
}
});
}
- else
- {
- // Open jalviewLite immediately.
- LoadingThread loader = new LoadingThread(file, applet);
- loader.start();
- }
}
else
{
// still be called to open new alignments.
file = "NO FILE";
fileFound = false;
+ callInitCallback();
+ }
+ }
+
+ private void initLiveConnect()
+ {
+ // try really hard to get the liveConnect thing working
+ boolean notFailed = false;
+ int tries = 0;
+ while (!notFailed && tries < 10)
+ {
+ if (tries > 0)
+ {
+ System.err.println("LiveConnect request thread going to sleep.");
+ }
+ try
+ {
+ Thread.sleep(700 * (1 + tries));
+ } catch (InterruptedException q)
+ {
+ }
+ ;
+ if (tries++ > 0)
+ {
+ System.err.println("LiveConnect request thread woken up.");
+ }
+ try
+ {
+ JSObject scriptObject = JSObject.getWindow(this);
+ if (scriptObject.eval("navigator") != null)
+ {
+ notFailed = true;
+ }
+ } catch (Exception jsex)
+ {
+ System.err.println("Attempt " + tries
+ + " to access LiveConnect javascript failed.");
+ }
+ }
+ }
+
+ private void callInitCallback()
+ {
+ String initjscallback = getParameter("oninit");
+ if (initjscallback == null)
+ {
+ return;
+ }
+ initjscallback = initjscallback.trim();
+ if (initjscallback.length() > 0)
+ {
+ JSObject scriptObject = null;
+ try
+ {
+ scriptObject = JSObject.getWindow(this);
+ } catch (Exception ex)
+ {
+ }
+ ;
+ // try really hard to let the browser plugin know we want liveconnect
+ initLiveConnect();
+
+ if (scriptObject != null)
+ {
+ try
+ {
+ // do onInit with the JS executor thread
+ new JSFunctionExec(this).executeJavascriptFunction(true,
+ initjscallback, null, "Calling oninit callback '"
+ + initjscallback + "'.");
+ } catch (Exception e)
+ {
+ System.err.println("Exception when executing _oninit callback '"
+ + initjscallback + "'.");
+ e.printStackTrace();
+ }
+ }
+ else
+ {
+ System.err.println("Not executing _oninit callback '"
+ + initjscallback + "' - no scripting allowed.");
+ }
}
}
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);
* @param g
* 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;
+ @Override
public void run()
{
if (running || checkedForJmol)
class LoadingThread extends Thread
{
/**
- * State variable: File source
- */
- String file;
-
- /**
* State variable: protocol for access to file source
*/
String protocol;
- /**
- * State variable: format of file source
- */
- String format;
+ String _file; // alignment file or URL spec
- String _file;
+ String _file2; // second alignment file or URL spec
JalviewLite applet;
private 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"))
+ /*
+ * is it paste data?
+ */
+ if (path.startsWith("PASTE"))
{
- file = file.substring(5);
protocol = AppletFormatAdapter.PASTE;
+ return path.substring(5);
}
- else if (inArchive(file))
+
+ /*
+ * is it a URL?
+ */
+ if (path.indexOf("://") != -1)
{
- protocol = AppletFormatAdapter.CLASSLOADER;
+ protocol = AppletFormatAdapter.URL;
+ return path;
}
- else
+
+ /*
+ * try relative to document root
+ */
+ URL documentBase = getDocumentBase();
+ String withDocBase = resolveUrlForLocalOrAbsolute(path, documentBase);
+ if (HttpUtils.isValidUrl(withDocBase))
+ {
+ if (debug)
+ {
+ System.err.println("Prepended document base '" + documentBase
+ + "' to make: '" + withDocBase + "'");
+ }
+ protocol = AppletFormatAdapter.URL;
+ return withDocBase;
+ }
+
+ /*
+ * try relative to codebase (if different to document base)
+ */
+ URL codeBase = getCodeBase();
+ String withCodeBase = applet.resolveUrlForLocalOrAbsolute(path,
+ codeBase);
+ if (!withCodeBase.equals(withDocBase)
+ && HttpUtils.isValidUrl(withCodeBase))
{
- file = addProtocol(file);
protocol = AppletFormatAdapter.URL;
+ if (debug)
+ {
+ System.err.println("Prepended codebase '" + codeBase
+ + "' to make: '" + withCodeBase + "'");
+ }
+ return withCodeBase;
+ }
+
+ /*
+ * try locating by classloader; try this last so files in the directory
+ * are resolved using document base
+ */
+ if (inArchive(path))
+ {
+ protocol = AppletFormatAdapter.CLASSLOADER;
}
- dbgMsg("Protocol identified as '" + protocol + "'");
- return file;
+ return path;
}
- 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();
} catch (Exception e)
{
}
- ;
}
startLoading();
+ // applet.callInitCallback();
}
+ /**
+ * Load the alignment and any related files as specified by applet
+ * parameters
+ */
private void startLoading()
{
- AlignFrame newAlignFrame;
dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");
- file = setProtocolState(_file);
- format = new jalview.io.IdentifyFile().Identify(file, protocol);
- dbgMsg("File identified as '" + format + "'");
dbgMsg("Loading started.");
- Alignment al = null;
+
+ AlignFrame newAlignFrame = readAlignment(_file);
+ AlignFrame newAlignFrame2 = readAlignment(_file2);
+ if (newAlignFrame != null)
+ {
+ addToDisplay(newAlignFrame, newAlignFrame2);
+ loadTree(newAlignFrame);
+
+ loadScoreFile(newAlignFrame);
+
+ loadFeatures(newAlignFrame);
+
+ loadAnnotations(newAlignFrame);
+
+ loadJnetFile(newAlignFrame);
+
+ loadPdbFiles(newAlignFrame);
+ }
+ else
+ {
+ fileFound = false;
+ applet.remove(launcher);
+ applet.repaint();
+ }
+ callInitCallback();
+ }
+
+ /**
+ * Add an AlignFrame to the display; or if two are provided, a SplitFrame.
+ *
+ * @param af
+ * @param af2
+ */
+ public void addToDisplay(AlignFrame af, AlignFrame af2)
+ {
+ if (af2 != null)
+ {
+ AlignmentI al1 = af.viewport.getAlignment();
+ AlignmentI al2 = af2.viewport.getAlignment();
+ AlignmentI cdna = al1.isNucleotide() ? al1 : al2;
+ AlignmentI prot = al1.isNucleotide() ? al2 : al1;
+ if (AlignmentUtils.mapProteinAlignmentToCdna(prot, cdna))
+ {
+ al2.alignAs(al1);
+ SplitFrame sf = new SplitFrame(af, af2);
+ sf.addToDisplay(embedded, JalviewLite.this);
+ return;
+ }
+ else
+ {
+ String msg = "Could not map any sequence in " + af2.getTitle()
+ + " as "
+ + (al1.isNucleotide() ? "protein product" : "cDNA")
+ + " for " + af.getTitle();
+ System.err.println(msg);
+ }
+ }
+
+ af.addToDisplay(embedded);
+ }
+
+ /**
+ * Read the alignment file (from URL, text 'paste', or archive by
+ * classloader).
+ *
+ * @return
+ */
+ protected AlignFrame readAlignment(String fileParam)
+ {
+ if (fileParam == null)
+ {
+ return null;
+ }
+ String resolvedFile = resolveFileProtocol(fileParam);
+ String format = new IdentifyFile().identify(resolvedFile, protocol);
+ dbgMsg("File identified as '" + format + "'");
+ AlignmentI al = null;
try
{
- al = new AppletFormatAdapter().readFile(file, protocol, 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 == AppletFormatAdapter.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.");
{
try
{
- FileParse fp = new FileParse(file, protocol);
+ FileParse fp = new FileParse(resolvedFile, protocol);
String ln = null;
- dbgMsg(">>>Dumping contents of '" + file + "' " + "("
+ dbgMsg(">>>Dumping contents of '" + resolvedFile + "' " + "("
+ protocol + ")");
while ((ln = fp.nextLine()) != null)
{
}
}
}
- if ((al != null) && (al.getHeight() > 0))
+ return null;
+ }
+
+ /**
+ * Load PDBFiles if any specified by parameter(s). Returns true if loaded,
+ * else false.
+ *
+ * @param alignFrame
+ * @return
+ */
+ protected boolean loadPdbFiles(AlignFrame alignFrame)
+ {
+ boolean result = false;
+ /*
+ * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6 -
+ * related to JAL-434
+ */
+
+ applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",
+ false));
+ /*
+ * <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;
+ // Accumulate pdbs here if they are heading for the same view (if
+ // alignPdbStructures is true)
+ Vector pdbs = new Vector();
+ // create a lazy matcher if we're asked to
+ jalview.analysis.SequenceIdMatcher matcher = (applet
+ .getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher(
+ alignFrame.getAlignViewport().getAlignment()
+ .getSequencesArray()) : null;
+
+ String param;
+ do
{
- dbgMsg("Successfully loaded file.");
- newAlignFrame = new AlignFrame(al, applet, file, embedded);
- if (initialAlignFrame == null)
+ if (pdbFileCount > 0)
{
- initialAlignFrame = newAlignFrame;
+ param = applet.getParameter("PDBFILE" + pdbFileCount);
}
- // update the focus.
- currentAlignFrame = newAlignFrame;
-
- if (protocol == jalview.io.AppletFormatAdapter.PASTE)
+ else
{
- newAlignFrame.setTitle("Sequences from " + getDocumentBase());
+ param = applet.getParameter("PDBFILE");
}
- newAlignFrame.statusBar.setText("Successfully loaded file " + file);
-
- String treeFile = applet.getParameter("tree");
- if (treeFile == null)
+ if (param != null)
{
- treeFile = applet.getParameter("treeFile");
- }
+ PDBEntry pdb = new PDBEntry();
- if (treeFile != null)
- {
- try
+ String seqstring;
+ SequenceI[] seqs = null;
+ String[] chains = null;
+
+ StringTokenizer st = new StringTokenizer(param, " ");
+
+ if (st.countTokens() < 2)
{
- 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)
+ String sequence = applet.getParameter("PDBSEQ");
+ if (sequence != null)
{
- newAlignFrame.loadTree(fin, treeFile);
- dbgMsg("Successfuly imported tree.");
+ seqs = new SequenceI[] { matcher == null ? (Sequence) alignFrame
+ .getAlignViewport().getAlignment().findName(sequence)
+ : matcher.findIdMatch(sequence) };
}
- else
- {
- dbgMsg("Tree parameter did not resolve to a valid tree.");
- }
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- String param = getParameter("features");
- if (param != null)
- {
- param = setProtocolState(param);
-
- newAlignFrame.parseFeaturesFile(param, protocol);
- }
-
- param = getParameter("showFeatureSettings");
- if (param != null && param.equalsIgnoreCase("true"))
- {
- newAlignFrame.viewport.showSequenceFeatures(true);
- new FeatureSettings(newAlignFrame.alignPanel);
- }
-
- param = getParameter("annotations");
- if (param != null)
- {
- param = setProtocolState(param);
-
- if (new AnnotationFile().readAnnotationFile(
- newAlignFrame.viewport.getAlignment(), param, protocol))
- {
- newAlignFrame.alignPanel.fontChanged();
- newAlignFrame.alignPanel.setScrollValues(0, 0);
- }
- else
- {
- System.err
- .println("Annotations were not added from annotation file '"
- + param + "'");
- }
- }
-
- param = getParameter("jnetfile");
- if (param != null)
- {
- try
- {
- param = setProtocolState(param);
- jalview.io.JPredFile predictions = new jalview.io.JPredFile(
- param, protocol);
- JnetAnnotationMaker.add_annotation(predictions,
- newAlignFrame.viewport.getAlignment(), 0, false); // false==do
- // not
- // add
- // sequence
- // profile
- // from
- // concise
- // output
- newAlignFrame.alignPanel.fontChanged();
- newAlignFrame.alignPanel.setScrollValues(0, 0);
- } catch (Exception ex)
- {
- ex.printStackTrace();
}
- }
- /*
- * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6
- * - related to JAL-434
- */
- applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",
- false));
- /*
- * <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;
- // Accumulate pdbs here if they are heading for the same view (if
- // alignPdbStructures is true)
- Vector pdbs = new Vector();
- do
- {
- if (pdbFileCount > 0)
- param = getParameter("PDBFILE" + pdbFileCount);
else
- param = getParameter("PDBFILE");
-
- if (param != null)
{
- PDBEntry pdb = new PDBEntry();
-
- String seqstring;
- SequenceI[] seqs = null;
- String[] chains = null;
-
- StringTokenizer st = new StringTokenizer(param, " ");
-
- if (st.countTokens() < 2)
- {
- String sequence = applet.getParameter("PDBSEQ");
- if (sequence != null)
- seqs = new SequenceI[]
- { (Sequence) newAlignFrame.getAlignViewport()
- .getAlignment().findName(sequence) };
+ param = st.nextToken();
+ List<SequenceI> tmp = new ArrayList<SequenceI>();
+ List<String> tmp2 = new ArrayList<String>();
- }
- else
+ while (st.hasMoreTokens())
{
- 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)
{
- seqstring = st.nextToken();
- StringTokenizer st2 = new StringTokenizer(seqstring, "=");
- if (st2.countTokens() > 1)
- {
- // This is the chain
- tmp2.addElement(st2.nextToken());
- seqstring = st2.nextToken();
- }
- tmp.addElement((Sequence) newAlignFrame.getAlignViewport()
- .getAlignment().findName(seqstring));
- }
-
- seqs = new SequenceI[tmp.size()];
- tmp.copyInto(seqs);
- if (tmp2.size() == tmp.size())
- {
- chains = new String[tmp2.size()];
- tmp2.copyInto(chains);
+ // This is the chain
+ tmp2.add(st2.nextToken());
+ seqstring = st2.nextToken();
}
+ tmp.add(matcher == null ? (Sequence) alignFrame
+ .getAlignViewport().getAlignment()
+ .findName(seqstring) : matcher.findIdMatch(seqstring));
}
- param = setProtocolState(param);
- if (// !jmolAvailable
- // &&
- protocol == AppletFormatAdapter.CLASSLOADER)
+ seqs = tmp.toArray(new SequenceI[tmp.size()]);
+ if (tmp2.size() == tmp.size())
{
- // 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); //
+ chains = tmp2.toArray(new String[tmp2.size()]);
}
+ }
+ param = resolveFileProtocol(param);
+ // TODO check JAL-357 for files in a jar (CLASSLOADER)
+ pdb.setFile(param);
- pdb.setFile(param);
-
- if (seqs != null)
+ if (seqs != null)
+ {
+ for (int i = 0; i < seqs.length; i++)
{
- for (int i = 0; i < seqs.length; i++)
- {
- if (seqs[i] != null)
- {
- ((Sequence) seqs[i]).addPDBId(pdb);
- }
- else
- {
- if (JalviewLite.debug)
- {
- // this may not really be a problem but we give a warning
- // anyway
- System.err
- .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
- + i + ")");
- }
- }
- }
-
- if (!alignPdbStructures)
+ if (seqs[i] != null)
{
- newAlignFrame.newStructureView(applet, pdb, seqs, chains,
- protocol);
+ ((Sequence) seqs[i]).addPDBId(pdb);
+ StructureSelectionManager.getStructureSelectionManager(
+ applet).registerPDBEntry(pdb);
}
else
{
- pdbs.addElement(new Object[]
- { pdb, seqs, chains, new String(protocol) });
+ if (JalviewLite.debug)
+ {
+ // this may not really be a problem but we give a warning
+ // anyway
+ System.err
+ .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
+ + i + ")");
+ }
}
}
+
+ if (!alignPdbStructures)
+ {
+ alignFrame.newStructureView(applet, pdb, seqs, chains,
+ protocol);
+ }
+ else
+ {
+ pdbs.addElement(new Object[] { pdb, seqs, chains,
+ new String(protocol) });
+ }
}
+ }
- pdbFileCount++;
- } while (pdbFileCount < 10);
- if (pdbs.size() > 0)
+ pdbFileCount++;
+ } while (param != null || pdbFileCount < 10);
+ if (pdbs.size() > 0)
+ {
+ SequenceI[][] seqs = new SequenceI[pdbs.size()][];
+ PDBEntry[] pdb = new PDBEntry[pdbs.size()];
+ String[][] chains = new String[pdbs.size()][];
+ String[] protocols = new String[pdbs.size()];
+ for (int pdbsi = 0, pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)
{
- SequenceI[][] seqs = new SequenceI[pdbs.size()][];
- PDBEntry[] pdb = new PDBEntry[pdbs.size()];
- String[][] chains = new String[pdbs.size()][];
- String[] protocols = new String[pdbs.size()];
- for (int pdbsi = 0, pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)
- {
- Object[] o = (Object[]) pdbs.elementAt(pdbsi);
- pdb[pdbsi] = (PDBEntry) o[0];
- seqs[pdbsi] = (SequenceI[]) o[1];
- chains[pdbsi] = (String[]) o[2];
- protocols[pdbsi] = (String) o[3];
- }
- newAlignFrame.alignedStructureView(applet, pdb, seqs, chains,
- protocols);
+ Object[] o = (Object[]) pdbs.elementAt(pdbsi);
+ pdb[pdbsi] = (PDBEntry) o[0];
+ seqs[pdbsi] = (SequenceI[]) o[1];
+ chains[pdbsi] = (String[]) o[2];
+ protocols[pdbsi] = (String) o[3];
+ }
+ alignFrame.alignedStructureView(applet, pdb, seqs, chains,
+ protocols);
+ result = true;
+ }
+ return result;
+ }
+ /**
+ * Load in a Jnetfile if specified by parameter. Returns true if loaded,
+ * else false.
+ *
+ * @param alignFrame
+ * @return
+ */
+ protected boolean loadJnetFile(AlignFrame alignFrame)
+ {
+ boolean result = false;
+ String param = applet.getParameter("jnetfile");
+ if (param != null)
+ {
+ try
+ {
+ param = resolveFileProtocol(param);
+ JPredFile predictions = new JPredFile(param, protocol);
+ JnetAnnotationMaker.add_annotation(predictions,
+ alignFrame.viewport.getAlignment(), 0, false);
+ // false == do not add sequence profile from concise output
+ SequenceI repseq = alignFrame.viewport.getAlignment()
+ .getSequenceAt(0);
+ alignFrame.viewport.getAlignment().setSeqrep(repseq);
+ ColumnSelection cs = new ColumnSelection();
+ cs.hideInsertionsFor(repseq);
+ alignFrame.viewport.setColumnSelection(cs);
+ alignFrame.alignPanel.fontChanged();
+ alignFrame.alignPanel.setScrollValues(0, 0);
+ result = true;
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
}
- // ///////////////////////////
- // modify display of features
- //
- // hide specific groups
- param = getParameter("hidefeaturegroups");
- if (param != null)
+ }
+ return result;
+ }
+
+ /**
+ * Load annotations if specified by parameter. Returns true if loaded, else
+ * false.
+ *
+ * @param alignFrame
+ * @return
+ */
+ protected boolean loadAnnotations(AlignFrame alignFrame)
+ {
+ boolean result = false;
+ String param = applet.getParameter("annotations");
+ if (param != null)
+ {
+ param = resolveFileProtocol(param);
+
+ if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
+ param, protocol))
{
- applet.setFeatureGroupStateOn(newAlignFrame, param, false);
+ alignFrame.alignPanel.fontChanged();
+ alignFrame.alignPanel.setScrollValues(0, 0);
+ result = true;
}
- // show specific groups
- param = getParameter("showfeaturegroups");
- if (param != null)
+ else
{
- applet.setFeatureGroupStateOn(newAlignFrame, param, true);
+ System.err
+ .println("Annotations were not added from annotation file '"
+ + param + "'");
}
}
- else
+ return result;
+ }
+
+ /**
+ * Load features file and view settings as specified by parameters. Returns
+ * true if features were loaded, else false.
+ *
+ * @param alignFrame
+ * @return
+ */
+ protected boolean loadFeatures(AlignFrame alignFrame)
+ {
+ boolean result = false;
+ // ///////////////////////////
+ // modify display of features
+ // we do this before any features have been loaded, ensuring any hidden
+ // groups are hidden when features first displayed
+ //
+ // hide specific groups
+ //
+ String param = applet.getParameter("hidefeaturegroups");
+ if (param != null)
{
- fileFound = false;
- remove(launcher);
- repaint();
+ alignFrame.setFeatureGroupState(separatorListToArray(param), false);
+ // applet.setFeatureGroupStateOn(newAlignFrame, param, false);
+ }
+ // show specific groups
+ param = applet.getParameter("showfeaturegroups");
+ if (param != null)
+ {
+ alignFrame.setFeatureGroupState(separatorListToArray(param), true);
+ // applet.setFeatureGroupStateOn(newAlignFrame, param, true);
+ }
+ // and now load features
+ param = applet.getParameter("features");
+ if (param != null)
+ {
+ param = resolveFileProtocol(param);
+
+ result = alignFrame.parseFeaturesFile(param, protocol);
+ }
+
+ param = applet.getParameter("showFeatureSettings");
+ if (param != null && param.equalsIgnoreCase(TRUE))
+ {
+ alignFrame.viewport.setShowSequenceFeatures(true);
+ new FeatureSettings(alignFrame.alignPanel);
+ }
+ return result;
+ }
+
+ /**
+ * Load a score file if specified by parameter. Returns true if file was
+ * loaded, else false.
+ *
+ * @param alignFrame
+ */
+ protected boolean loadScoreFile(AlignFrame alignFrame)
+ {
+ boolean result = false;
+ String sScoreFile = applet.getParameter("scoreFile");
+ if (sScoreFile != null && !"".equals(sScoreFile))
+ {
+ try
+ {
+ if (debug)
+ {
+ System.err
+ .println("Attempting to load T-COFFEE score file from the scoreFile parameter");
+ }
+ result = alignFrame.loadScoreFile(sScoreFile);
+ if (!result)
+ {
+ System.err
+ .println("Failed to parse T-COFFEE parameter as a valid score file ('"
+ + sScoreFile + "')");
+ }
+ } catch (Exception e)
+ {
+ System.err.printf("Cannot read score file: '%s'. Cause: %s \n",
+ sScoreFile, e.getMessage());
+ }
}
+ return result;
+ }
+
+ /**
+ * Load a tree for the alignment if specified by parameter. Returns true if
+ * a tree was loaded, else false.
+ *
+ * @param alignFrame
+ * @return
+ */
+ protected boolean loadTree(AlignFrame alignFrame)
+ {
+ boolean result = false;
+ String treeFile = applet.getParameter("tree");
+ if (treeFile == null)
+ {
+ treeFile = applet.getParameter("treeFile");
+ }
+
+ if (treeFile != null)
+ {
+ try
+ {
+ treeFile = resolveFileProtocol(treeFile);
+ NewickFile fin = new NewickFile(treeFile, protocol);
+ fin.parse();
+
+ if (fin.getTree() != null)
+ {
+ alignFrame.loadTree(fin, treeFile);
+ result = true;
+ dbgMsg("Successfully imported tree.");
+ }
+ else
+ {
+ dbgMsg("Tree parameter did not resolve to a valid tree.");
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ return result;
}
/**
* Discovers whether the given file is in the Applet Archive
*
- * @param file
+ * @param f
* String
* @return boolean
*/
- boolean inArchive(String file)
+ boolean inArchive(String f)
{
// This might throw a security exception in certain browsers
// Netscape Communicator for instance.
try
{
- boolean rtn = (getClass().getResourceAsStream("/" + file) != null);
+ boolean rtn = (getClass().getResourceAsStream("/" + f) != null);
if (debug)
{
- System.err.println("Resource '" + file + "' was "
- + (rtn ? "" : "not") + " located by classloader.");
+ System.err.println("Resource '" + f + "' was "
+ + (rtn ? "" : "not ") + "located by classloader.");
}
return rtn;
} catch (Exception ex)
{
- System.out.println("Exception checking resources: " + file + " "
- + ex);
+ System.out.println("Exception checking resources: " + f + " " + ex);
return false;
}
}
-
- String addProtocol(String file)
- {
- if (file.indexOf("://") == -1)
- {
- file = getCodeBase() + file;
- if (debug)
- {
- System.err.println("Prepended codebase for resource: '" + file
- + "'");
- }
- }
-
- return file;
- }
}
/**
* return null with an error message on System.err indicating the
* fact.
*/
- protected AlignFrame getDefaultTargetFrame()
+ public AlignFrame getDefaultTargetFrame()
{
if (currentAlignFrame != 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
+ */
+ public boolean jsfallbackEnabled = false;
/**
* parse the string into a list
* @param separator
* @return elements separated by separator
*/
- public String[] separatorListToArray(String list, String separator)
+ public static String[] separatorListToArray(String list, String separator)
{
- // note separator local variable intentionally masks object field
+ // TODO use StringUtils version (slightly different...)
int seplen = separator.length();
if (list == null || list.equals("") || list.equals(separator))
+ {
return null;
+ }
java.util.Vector jv = new Vector();
int cp = 0, pos;
while ((pos = list.indexOf(separator, cp)) > cp)
}
if (cp < list.length())
{
- jv.addElement(list.substring(cp));
+ String c = list.substring(cp);
+ if (!c.equals(separator))
+ {
+ jv.addElement(c);
+ }
}
if (jv.size() > 0)
{
* @param separator
* @return concatenated string
*/
- public String arrayToSeparatorList(String[] list, String separator)
+ public static String arrayToSeparatorList(String[] list, String separator)
{
+ // TODO use StringUtils version
StringBuffer v = new StringBuffer();
if (list != null && list.length > 0)
{
- for (int i = 0, iSize = list.length - 1; i < iSize; i++)
+ for (int i = 0, iSize = list.length; i < iSize; i++)
{
if (list[i] != null)
{
+ if (i > 0)
+ {
+ v.append(separator);
+ }
v.append(list[i]);
}
- v.append(separator);
- }
- if (list[list.length - 1] != null)
- {
- v.append(list[list.length - 1]);
}
if (debug)
{
return "" + separator;
}
- /**
- * @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroups()
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
*/
+ @Override
public String getFeatureGroups()
{
String lst = arrayToSeparatorList(getDefaultTargetFrame()
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
+ * )
*/
+ @Override
public String getFeatureGroupsOn(AlignFrame alf)
{
String lst = arrayToSeparatorList(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));
}
- /**
- * @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)
*/
+ @Override
public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
{
return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
}
- /**
- * @param groups
- * tab separated list of group names
- * @param state
- * true or false
- * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[],
- * boolean)
+ /*
+ * (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 AlignFrame 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()
+ {
+ 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 + "'");
+ }
}
/**
{
return def;
}
- if (stn.toLowerCase().equals("true"))
+ if (TRUE.equalsIgnoreCase(stn))
{
return true;
}
return false;
}
- /**
- * bind a pdb file to a sequence in the given alignFrame.
+ /*
+ * (non-Javadoc)
*
- * @param alFrame
- * - null or specific alignFrame. This specifies the dataset that
- * will be searched for a seuqence called sequenceId
- * @param sequenceId
- * - sequenceId within the dataset.
- * @param pdbEntryString
- * - the short name for the PDB file
- * @param pdbFile
- * - pdb file - either a URL or a valid PDB file.
- * @return true if binding was as success TODO: consider making an exception
- * structure for indicating when PDB parsing or seqeunceId location
- * fails.
+ * @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame,
+ * java.lang.String, java.lang.String, java.lang.String)
*/
+ @Override
public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
String pdbEntryString, String pdbFile)
{
return alignPdbStructures;
}
+ @Override
+ public void start()
+ {
+ // callInitCallback();
+ }
+
+ private Hashtable<String, long[]> jshashes = new Hashtable<String, long[]>();
+
+ private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<String, Hashtable<String, String[]>>();
+
+ public void setJsMessageSet(String messageclass, String viewId,
+ String[] colcommands)
+ {
+ Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
+ if (msgset == null)
+ {
+ msgset = new Hashtable<String, String[]>();
+ jsmessages.put(messageclass, msgset);
+ }
+ msgset.put(viewId, colcommands);
+ long[] l = new long[colcommands.length];
+ for (int i = 0; i < colcommands.length; i++)
+ {
+ l[i] = colcommands[i].hashCode();
+ }
+ jshashes.put(messageclass + "|" + viewId, l);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String,
+ * java.lang.String)
+ */
+ @Override
+ public String getJsMessage(String messageclass, String viewId)
+ {
+ Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
+ if (msgset != null)
+ {
+ String[] msgs = msgset.get(viewId);
+ if (msgs != null)
+ {
+ for (int i = 0; i < msgs.length; i++)
+ {
+ if (msgs[i] != null)
+ {
+ String m = msgs[i];
+ msgs[i] = null;
+ return m;
+ }
+ }
+ }
+ }
+ return "";
+ }
+
+ public boolean isJsMessageSetChanged(String string, String string2,
+ String[] colcommands)
+ {
+ long[] l = jshashes.get(string + "|" + string2);
+ if (l == null && colcommands != null)
+ {
+ return true;
+ }
+ for (int i = 0; i < colcommands.length; i++)
+ {
+ if (l[i] != colcommands[i].hashCode())
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ private Vector jsExecQueue = new Vector();
+
+ public Vector getJsExecQueue()
+ {
+ return jsExecQueue;
+ }
+
+ public void setExecutor(JSFunctionExec jsFunctionExec2)
+ {
+ jsFunctionExec = jsFunctionExec2;
+ }
+
/**
- * get all components associated with the applet of the given type
+ * return the given colour value parameter or the given default if parameter
+ * not given
*
- * @param class1
+ * @param colparam
+ * @param defcolour
* @return
*/
- public Vector getAppletWindow(Class class1)
+ public Color getDefaultColourParameter(String colparam, Color defcolour)
{
- Vector wnds = new Vector();
- Component[] cmp = getComponents();
- if (cmp != null)
+ String colprop = getParameter(colparam);
+ if (colprop == null || colprop.trim().length() == 0)
{
- for (int i = 0; i < cmp.length; i++)
+ return defcolour;
+ }
+ Color col = jalview.schemes.ColourSchemeProperty
+ .getAWTColorFromName(colprop);
+ if (col == null)
+ {
+ try
{
- if (class1.isAssignableFrom(cmp[i].getClass()))
+ col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
+ } catch (Exception ex)
+ {
+ System.err.println("Couldn't parse '" + colprop
+ + "' as a colour for " + colparam);
+ col = null;
+ }
+ }
+ return (col == null) ? defcolour : col;
+
+ }
+
+ public void openJalviewHelpUrl()
+ {
+ String helpUrl = getParameter("jalviewhelpurl");
+ if (helpUrl == null || helpUrl.trim().length() < 5)
+ {
+ helpUrl = "http://www.jalview.org/help.html";
+ }
+ showURL(helpUrl, "HELP");
+ }
+
+ /**
+ * form a complete URL given a path to a resource and a reference location on
+ * the same server
+ *
+ * @param targetPath
+ * - an absolute path on the same server as localref or a document
+ * located relative to localref
+ * @param localref
+ * - a URL on the same server as url
+ * @return a complete URL for the resource located by url
+ */
+ private String resolveUrlForLocalOrAbsolute(String targetPath,
+ URL localref)
+ {
+ String resolvedPath = "";
+ if (targetPath.startsWith("/"))
+ {
+ String codebase = localref.toString();
+ String localfile = localref.getFile();
+ resolvedPath = codebase.substring(0,
+ codebase.length() - localfile.length())
+ + targetPath;
+ return resolvedPath;
+ }
+
+ /*
+ * get URL path and strip off any trailing file e.g.
+ * www.jalview.org/examples/index.html#applets?a=b is trimmed to
+ * www.jalview.org/examples/
+ */
+ String urlPath = localref.toString();
+ String directoryPath = urlPath;
+ int lastSeparator = directoryPath.lastIndexOf("/");
+ if (lastSeparator > 0)
+ {
+ directoryPath = directoryPath.substring(0, lastSeparator + 1);
+ }
+
+ if (targetPath.startsWith("/"))
+ {
+ /*
+ * construct absolute URL to a file on the server - this is not allowed?
+ */
+ // String localfile = localref.getFile();
+ // resolvedPath = urlPath.substring(0,
+ // urlPath.length() - localfile.length())
+ // + targetPath;
+ resolvedPath = directoryPath + targetPath.substring(1);
+ }
+ else
+ {
+ resolvedPath = directoryPath + targetPath;
+ }
+ if (debug)
+ {
+ System.err.println("resolveUrlForLocalOrAbsolute returning "
+ + resolvedPath);
+ }
+ return resolvedPath;
+ }
+
+ /**
+ * open a URL in the browser - resolving it according to relative refs and
+ * coping with javascript: protocol if necessary.
+ *
+ * @param url
+ * @param target
+ */
+ public void showURL(String url, String target)
+ {
+ try
+ {
+ if (url.indexOf(":") == -1)
+ {
+ // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
+ // form valid URL
+ // Should really use docbase, not codebase.
+ URL prepend;
+ url = resolveUrlForLocalOrAbsolute(
+ url,
+ prepend = getDefaultParameter("resolvetocodebase", false) ? getCodeBase()
+ : getDocumentBase());
+ if (debug)
{
- wnds.addElement(cmp);
+ 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();
}
- return wnds;
}
/**
git://source.jalview.org / jalview.git / blobdiff