X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=dcd326110478d7b89dcacfe5a6c8997fd01c33b2;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=378376b1e0f4519f0a14d4c74793c49d5e9ac221;hpb=e093944b00cb26f22062033be8992df42340ef00;p=jalview.git
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
old mode 100755
new mode 100644
index 378376b..dcd3261
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1,27 +1,33 @@
/*
- * 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 2.8.2b1)
+ * Copyright (C) 2014 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
+import jalview.api.StructureSelectionManagerProvider;
import jalview.appletgui.AlignFrame;
+import jalview.appletgui.AlignViewport;
import jalview.appletgui.EmbmenuFrame;
import jalview.appletgui.FeatureSettings;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
@@ -32,14 +38,18 @@ import jalview.io.AppletFormatAdapter;
import jalview.io.FileParse;
import jalview.io.IdentifyFile;
import jalview.io.JnetAnnotationMaker;
+import jalview.javascript.JSFunctionExec;
+import jalview.javascript.JalviewLiteJsApi;
import jalview.javascript.JsCallBack;
import jalview.structure.SelectionListener;
import jalview.structure.StructureSelectionManager;
+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;
@@ -48,68 +58,77 @@ import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.io.BufferedReader;
import java.io.InputStreamReader;
+import java.net.URL;
+import java.util.Hashtable;
import java.util.StringTokenizer;
import java.util.Vector;
+import netscape.javascript.JSException;
+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
{
+ public StructureSelectionManager getStructureSelectionManager()
+ {
+ return StructureSelectionManager.getStructureSelectionManager(this);
+ }
+
// /////////////////////////////////////////
// The following public methods maybe 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()
*/
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)
*/
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)
{
- 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)
{
StringBuffer result = new StringBuffer("");
if (sep == null || sep.length() == 0)
{
- sep = "¬";
+ sep = separator; // "+0x00AC;
}
if (alf.viewport.getSelectionGroup() != null)
{
@@ -126,122 +145,157 @@ public class JalviewLite extends Applet
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)
+ 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)
+ 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)
*/
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)
*/
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)
+ 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)
+ 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;
@@ -333,10 +387,18 @@ public class JalviewLite extends Applet
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)
{
@@ -373,43 +435,59 @@ public class JalviewLite extends Applet
}
}
}
- 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);
+ if (csel != null)
+ {
+ Vector cs = csel.getSelected();
+ csel.clear();
+ for (int csi = 0, csiS = cs.size(); csi < csiS; csi++)
+ {
+ csel.addElement(rs.findIndex(((Integer) cs.elementAt(csi))
+ .intValue()));
+ }
+ }
+ }
+ 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)
*/
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)
*/
public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
String format, String suffix)
@@ -419,6 +497,9 @@ public class JalviewLite extends Applet
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);
@@ -432,21 +513,166 @@ public class JalviewLite extends Applet
return "";
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder()
+ */
+ public String getAlignmentOrder()
+ {
+ return getAlignmentOrderFrom(getDefaultTargetFrame());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
+ * )
+ */
+ public String getAlignmentOrderFrom(AlignFrame alf)
+ {
+ return getAlignmentOrderFrom(alf, separator);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
+ * , java.lang.String)
+ */
+ 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)
+ */
+ 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)
+ */
+ 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)
+ */
+ 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)
+ */
public String getAlignment(String format)
{
return getAlignmentFrom(getDefaultTargetFrame(), format, "true");
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
+ * java.lang.String)
+ */
public String getAlignmentFrom(AlignFrame alf, String format)
{
return getAlignmentFrom(alf, format, "true");
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String,
+ * java.lang.String)
+ */
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)
+ */
public String getAlignmentFrom(AlignFrame alf, String format,
String suffix)
{
@@ -464,11 +690,23 @@ public class JalviewLite extends Applet
}
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
+ */
public void loadAnnotation(String annotation)
{
loadAnnotationFrom(getDefaultTargetFrame(), annotation);
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
+ * , java.lang.String)
+ */
public void loadAnnotationFrom(AlignFrame alf, String annotation)
{
if (new AnnotationFile().readAnnotationFile(alf.getAlignViewport()
@@ -483,53 +721,120 @@ public class JalviewLite extends Applet
}
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
+ */
+ public void loadFeatures(String features, boolean autoenabledisplay)
+ {
+ loadFeaturesFrom(getDefaultTargetFrame(), features, autoenabledisplay);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
+ * , java.lang.String)
+ */
+ 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)
+ */
public String getFeatures(String format)
{
return getFeaturesFrom(getDefaultTargetFrame(), format);
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame,
+ * java.lang.String)
+ */
public String getFeaturesFrom(AlignFrame alf, String format)
{
return alf.outputFeatures(false, format);
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getAnnotation()
+ */
public String getAnnotation()
{
return getAnnotationFrom(getDefaultTargetFrame());
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame
+ * )
+ */
public String getAnnotationFrom(AlignFrame alf)
{
return alf.outputAnnotations(false);
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#newView()
+ */
public AlignFrame newView()
{
return newViewFrom(getDefaultTargetFrame());
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String)
+ */
public AlignFrame newView(String name)
{
return newViewFrom(getDefaultTargetFrame(), name);
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame)
+ */
public AlignFrame newViewFrom(AlignFrame alf)
{
return alf.newView(null);
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame,
+ * java.lang.String)
+ */
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)
*/
public AlignFrame loadAlignment(String text, String title)
{
@@ -552,13 +857,25 @@ public class JalviewLite extends Applet
return null;
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String)
+ */
public void setMouseoverListener(String listener)
{
setMouseoverListener(currentAlignFrame, listener);
}
- private Vector mouseoverListeners = new Vector();
+ private Vector javascriptListeners = new Vector();
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame
+ * , java.lang.String)
+ */
public void setMouseoverListener(AlignFrame af, String listener)
{
if (listener != null)
@@ -573,24 +890,36 @@ public class JalviewLite extends Applet
}
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)
+ */
public void setSelectionListener(String listener)
{
setSelectionListener(null, listener);
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame
+ * , java.lang.String)
+ */
public void setSelectionListener(AlignFrame af, String listener)
{
if (listener != null)
@@ -605,27 +934,57 @@ public class JalviewLite extends Applet
}
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)
+ /*
+ * (non-Javadoc)
*
- * @param af
- * (may be null)
- * @param listener
- * (may be null)
+ * @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String,
+ * java.lang.String)
+ */
+ 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;
+ }
+ }
+ jalview.javascript.MouseOverStructureListener mol = new jalview.javascript.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)
*/
public void removeJavascriptListener(AlignFrame af, String listener)
{
@@ -638,24 +997,24 @@ public class JalviewLite extends Applet
}
}
boolean rprt = false;
- for (int ms=0,msSize=mouseoverListeners.size();ms0)
+ 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)
+ 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)
+ */
+ 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());
+
+ } catch (Exception ex)
+ {
+ System.err.println("Couldn't parse integer arguments (topRow='"
+ + topRow + "' and leftHandColumn='" + leftHandColumn
+ + "')");
+ ex.printStackTrace();
+ }
+ }
+ });
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.javascript.JalviewLiteJsApi#scrollViewToRowIn(jalview.appletgui
+ * .AlignFrame, java.lang.String)
+ */
+ @Override
+ public void scrollViewToRowIn(final AlignFrame alf, final String topRow)
+ {
+
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ try
+ {
+ alf.scrollToRow(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 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();
+ }
+ }
+ });
+
}
// //////////////////////////////////////////////
@@ -724,7 +1241,7 @@ public class JalviewLite extends Applet
* AlignFrame if the applet is started as embedded on the page and then
* afterwards a new view is created.
*/
- public static AlignFrame currentAlignFrame = null;
+ public AlignFrame currentAlignFrame = null;
/**
* This is the first frame to be displayed, and does not change. API calls
@@ -744,9 +1261,15 @@ public class JalviewLite extends Applet
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()
{
@@ -754,6 +1277,7 @@ public class JalviewLite extends Applet
{
builddate = "unknown";
version = "test";
+ installation = "Webstart";
java.net.URL url = JalviewLite.class
.getResource("/.build_properties");
if (url != null)
@@ -773,6 +1297,10 @@ public class JalviewLite extends Applet
{
builddate = line.substring(line.indexOf("=") + 1);
}
+ if (line.indexOf("INSTALLATION") > -1)
+ {
+ installation = line.substring(line.indexOf("=") + 1);
+ }
}
} catch (Exception ex)
{
@@ -788,19 +1316,48 @@ public class JalviewLite extends Applet
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
*/
public void init()
{
// remove any handlers that might be hanging around from an earlier instance
-
+ 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();
+ }
+ }
/**
* turn on extra applet debugging
*/
@@ -814,8 +1371,15 @@ public class JalviewLite extends Applet
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
*/
@@ -840,8 +1404,7 @@ public class JalviewLite extends Applet
}
else
{
- throw new Error(
- "Invalid separator parameter - must be non-zero length");
+ throw new Error(MessageManager.getString("error.invalid_separator_parameter"));
}
}
int r = 255;
@@ -863,14 +1426,13 @@ public class JalviewLite extends Applet
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");
@@ -890,13 +1452,13 @@ public class JalviewLite extends Applet
}
}
- final JalviewLite applet = this;
+ final JalviewLite jvapplet = this;
if (getParameter("embedded") != null
&& getParameter("embedded").equalsIgnoreCase("true"))
{
// Launch as embedded applet in page
embedded = true;
- LoadingThread loader = new LoadingThread(file, applet);
+ LoadingThread loader = new LoadingThread(file, jvapplet);
loader.start();
}
else if (file != null)
@@ -908,27 +1470,109 @@ public class JalviewLite extends Applet
add(launcher);
launcher.addActionListener(new java.awt.event.ActionListener()
{
- public void actionPerformed(ActionEvent e)
- {
- LoadingThread loader = new LoadingThread(file, applet);
- loader.start();
- }
- });
+ public void actionPerformed(ActionEvent e)
+ {
+ LoadingThread loader = new LoadingThread(file, jvapplet);
+ loader.start();
+ }
+ });
+ }
+ else
+ {
+ // Open jalviewLite immediately.
+ LoadingThread loader = new LoadingThread(file, jvapplet);
+ loader.start();
+ }
+ }
+ else
+ {
+ // jalview initialisation with no alignment. loadAlignment() method can
+ // still be called to open new alignments.
+ file = "NO FILE";
+ fileFound = false;
+ callInitCallback();
+ }
+ }
+
+ private void initLiveConnect()
+ {
+ // try really hard to get the liveConnect thing working
+ boolean notFailed = false;
+ int tries = 0;
+ while (!notFailed && tries < 10)
+ {
+ if (tries > 0)
+ {
+ System.err.println("LiveConnect request thread going to sleep.");
+ }
+ try
+ {
+ Thread.sleep(700 * (1 + tries));
+ } catch (InterruptedException q)
+ {
+ }
+ ;
+ if (tries++ > 0)
+ {
+ System.err.println("LiveConnect request thread woken up.");
+ }
+ try
+ {
+ JSObject scriptObject = JSObject.getWindow(this);
+ if (scriptObject.eval("navigator") != null)
+ {
+ notFailed = true;
+ }
+ } catch (JSException 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
{
- // Open jalviewLite immediately.
- LoadingThread loader = new LoadingThread(file, applet);
- loader.start();
+ System.err.println("Not executing _oninit callback '"
+ + initjscallback + "' - no scripting allowed.");
}
}
- else
- {
- // jalview initialisation with no alignment. loadAlignment() method can
- // still be called to open new alignments.
- file = "NO FILE";
- fileFound = false;
- }
}
/**
@@ -957,11 +1601,15 @@ public class JalviewLite extends Applet
{
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;
@@ -977,7 +1625,7 @@ public class JalviewLite extends Applet
{
if (frame instanceof AlignFrame)
{
- currentAlignFrame = (AlignFrame) frame;
+ ((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame;
if (debug)
{
System.err.println("Activated window " + frame);
@@ -1018,16 +1666,43 @@ public class JalviewLite extends Applet
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
@@ -1156,6 +1831,7 @@ public class JalviewLite extends Applet
;
}
startLoading();
+ // applet.callInitCallback();
}
private void startLoading()
@@ -1209,10 +1885,14 @@ public class JalviewLite extends Applet
if (protocol == jalview.io.AppletFormatAdapter.PASTE)
{
- newAlignFrame.setTitle("Sequences from " + getDocumentBase());
+ newAlignFrame.setTitle(MessageManager.formatMessage(
+ "label.sequences_from", new String[]
+ { applet.getDocumentBase().toString() }));
}
- newAlignFrame.statusBar.setText("Successfully loaded file " + file);
+ newAlignFrame.statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_loaded_file", new String[]
+ { file }));
String treeFile = applet.getParameter("tree");
if (treeFile == null)
@@ -1250,7 +1930,56 @@ public class JalviewLite extends Applet
}
}
- String param = getParameter("features");
+ /*
+ * Try to load T-Coffee score file
+ */
+ 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");
+ }
+ if (!newAlignFrame.loadScoreFile(sScoreFile))
+ {
+ 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());
+ }
+ }
+
+ // ///////////////////////////
+ // 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)
+ {
+ newAlignFrame.setFeatureGroupState(separatorListToArray(param),
+ false);
+ // applet.setFeatureGroupStateOn(newAlignFrame, param, false);
+ }
+ // show specific groups
+ param = applet.getParameter("showfeaturegroups");
+ if (param != null)
+ {
+ newAlignFrame.setFeatureGroupState(separatorListToArray(param),
+ true);
+ // applet.setFeatureGroupStateOn(newAlignFrame, param, true);
+ }
+ // and now load features
+ param = applet.getParameter("features");
if (param != null)
{
param = setProtocolState(param);
@@ -1258,14 +1987,14 @@ public class JalviewLite extends Applet
newAlignFrame.parseFeaturesFile(param, protocol);
}
- param = getParameter("showFeatureSettings");
+ param = applet.getParameter("showFeatureSettings");
if (param != null && param.equalsIgnoreCase("true"))
{
newAlignFrame.viewport.showSequenceFeatures(true);
new FeatureSettings(newAlignFrame.alignPanel);
}
- param = getParameter("annotations");
+ param = applet.getParameter("annotations");
if (param != null)
{
param = setProtocolState(param);
@@ -1285,7 +2014,7 @@ public class JalviewLite extends Applet
}
- param = getParameter("jnetfile");
+ param = applet.getParameter("jnetfile");
if (param != null)
{
try
@@ -1328,12 +2057,22 @@ public class JalviewLite extends Applet
// 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(
+ newAlignFrame.getAlignViewport().getAlignment()
+ .getSequencesArray()) : null;
+
do
{
if (pdbFileCount > 0)
- param = getParameter("PDBFILE" + pdbFileCount);
+ {
+ param = applet.getParameter("PDBFILE" + pdbFileCount);
+ }
else
- param = getParameter("PDBFILE");
+ {
+ param = applet.getParameter("PDBFILE");
+ }
if (param != null)
{
@@ -1349,9 +2088,12 @@ public class JalviewLite extends Applet
{
String sequence = applet.getParameter("PDBSEQ");
if (sequence != null)
+ {
seqs = new SequenceI[]
- { (Sequence) newAlignFrame.getAlignViewport()
- .getAlignment().findName(sequence) };
+ { matcher == null ? (Sequence) newAlignFrame
+ .getAlignViewport().getAlignment()
+ .findName(sequence) : matcher.findIdMatch(sequence) };
+ }
}
else
@@ -1370,8 +2112,10 @@ public class JalviewLite extends Applet
tmp2.addElement(st2.nextToken());
seqstring = st2.nextToken();
}
- tmp.addElement((Sequence) newAlignFrame.getAlignViewport()
- .getAlignment().findName(seqstring));
+ tmp.addElement(matcher == null ? (Sequence) newAlignFrame
+ .getAlignViewport().getAlignment()
+ .findName(seqstring) : matcher
+ .findIdMatch(seqstring));
}
seqs = new SequenceI[tmp.size()];
@@ -1386,8 +2130,11 @@ public class JalviewLite extends Applet
if (// !jmolAvailable
// &&
- protocol == AppletFormatAdapter.CLASSLOADER)
+ protocol == AppletFormatAdapter.CLASSLOADER
+ && !useXtrnalSviewer)
{
+ // Re: JAL-357 : the bug isn't a problem if we are using an
+ // external viewer!
// TODO: verify this Re:
// https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
// This exception preserves the current behaviour where, even if
@@ -1406,6 +2153,8 @@ public class JalviewLite extends Applet
if (seqs[i] != null)
{
((Sequence) seqs[i]).addPDBId(pdb);
+ StructureSelectionManager.getStructureSelectionManager(
+ applet).registerPDBEntry(pdb);
}
else
{
@@ -1434,7 +2183,7 @@ public class JalviewLite extends Applet
}
pdbFileCount++;
- } while (pdbFileCount < 10);
+ } while (param != null || pdbFileCount < 10);
if (pdbs.size() > 0)
{
SequenceI[][] seqs = new SequenceI[pdbs.size()][];
@@ -1453,28 +2202,14 @@ public class JalviewLite extends Applet
protocols);
}
- // ///////////////////////////
- // modify display of features
- //
- // hide specific groups
- param = getParameter("hidefeaturegroups");
- if (param != null)
- {
- applet.setFeatureGroupStateOn(newAlignFrame, param, false);
- }
- // show specific groups
- param = getParameter("showfeaturegroups");
- if (param != null)
- {
- applet.setFeatureGroupStateOn(newAlignFrame, param, true);
- }
}
else
{
fileFound = false;
- remove(launcher);
- repaint();
+ applet.remove(launcher);
+ applet.repaint();
}
+ callInitCallback();
}
/**
@@ -1509,12 +2244,40 @@ public class JalviewLite extends Applet
{
if (file.indexOf("://") == -1)
{
- file = getCodeBase() + file;
- if (debug)
+ String fl = applet.resolveUrlForLocalOrAbsolute(file,
+ getDocumentBase());
+ try
+ {
+ if (new java.net.URL(fl).openStream() != null)
+ {
+ if (debug)
+ {
+ System.err.println("Prepended document base for resource: '"
+ + file + "'");
+ }
+ return fl;
+ }
+ } catch (Exception x)
+ {
+ }
+ ;
+ fl = applet.resolveUrlForLocalOrAbsolute(file, getCodeBase());
+ try
+ {
+ if (new java.net.URL(fl).openStream() != null)
+ {
+ if (debug)
+ {
+ System.err.println("Prepended codebase for resource: '"
+ + file + "'");
+ }
+ return fl;
+ }
+ } catch (Exception x)
{
- System.err.println("Prepended codebase for resource: '" + file
- + "'");
}
+ ;
+
}
return file;
@@ -1526,7 +2289,7 @@ public class JalviewLite extends Applet
* return null with an error message on System.err indicating the
* fact.
*/
- protected AlignFrame getDefaultTargetFrame()
+ public AlignFrame getDefaultTargetFrame()
{
if (currentAlignFrame != null)
{
@@ -1544,9 +2307,14 @@ public class JalviewLite extends Applet
/**
* 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
@@ -1571,7 +2339,9 @@ public class JalviewLite extends Applet
// note separator local variable intentionally masks object field
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)
@@ -1581,7 +2351,11 @@ public class JalviewLite extends Applet
}
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)
{
@@ -1633,17 +2407,16 @@ public class JalviewLite extends Applet
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)
{
@@ -1661,9 +2434,10 @@ public class JalviewLite extends Applet
return "" + separator;
}
- /**
- * @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroups()
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
*/
public String getFeatureGroups()
{
@@ -1672,11 +2446,12 @@ public class JalviewLite extends Applet
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)
{
@@ -1684,10 +2459,10 @@ public class JalviewLite extends Applet
return lst;
}
- /**
- * @param visible
- * @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)
*/
public String getFeatureGroupsOfState(boolean visible)
{
@@ -1695,58 +2470,77 @@ public class JalviewLite extends Applet
.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)
{
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)
+ 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)
+ */
public void setFeatureGroupState(String groups, boolean state)
{
setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
}
- /**
- * List separator string
+ /*
+ * (non-Javadoc)
*
- * @return the separator
+ * @see jalview.bin.JalviewLiteJsApi#getSeparator()
*/
public String getSeparator()
{
return separator;
}
- /**
- * List separator string
+ /*
+ * (non-Javadoc)
*
- * @param separator
- * the separator to set
+ * @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String)
*/
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 + "'");
+ }
}
/**
@@ -1773,21 +2567,11 @@ public class JalviewLite extends Applet
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)
*/
public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
String pdbEntryString, String pdbFile)
@@ -1805,27 +2589,211 @@ public class JalviewLite extends Applet
return alignPdbStructures;
}
+ public void start()
+ {
+ // callInitCallback();
+ }
+
+ private Hashtable jshashes = new Hashtable();
+
+ private Hashtable> jsmessages = new Hashtable>();
+
+ public void setJsMessageSet(String messageclass, String viewId,
+ String[] colcommands)
+ {
+ Hashtable msgset = jsmessages.get(messageclass);
+ if (msgset == null)
+ {
+ msgset = new Hashtable();
+ jsmessages.put(messageclass, msgset);
+ }
+ msgset.put(viewId, colcommands);
+ long[] l = new long[colcommands.length];
+ for (int i = 0; i < colcommands.length; i++)
+ {
+ l[i] = colcommands[i].hashCode();
+ }
+ jshashes.put(messageclass + "|" + viewId, l);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String,
+ * java.lang.String)
+ */
+ public String getJsMessage(String messageclass, String viewId)
+ {
+ Hashtable msgset = jsmessages.get(messageclass);
+ if (msgset != null)
+ {
+ String[] msgs = msgset.get(viewId);
+ if (msgs != null)
+ {
+ for (int i = 0; i < msgs.length; i++)
+ {
+ if (msgs[i] != null)
+ {
+ String m = msgs[i];
+ msgs[i] = null;
+ return m;
+ }
+ }
+ }
+ }
+ return "";
+ }
+
+ public boolean isJsMessageSetChanged(String string, String string2,
+ String[] colcommands)
+ {
+ long[] l = jshashes.get(string + "|" + string2);
+ if (l == null && colcommands != null)
+ {
+ return true;
+ }
+ for (int i = 0; i < colcommands.length; i++)
+ {
+ if (l[i] != colcommands[i].hashCode())
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ private Vector jsExecQueue = new Vector();
+
+ public Vector getJsExecQueue()
+ {
+ return jsExecQueue;
+ }
+
+ public void setExecutor(JSFunctionExec jsFunctionExec2)
+ {
+ jsFunctionExec = jsFunctionExec2;
+ }
+
/**
- * 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 url
+ * - 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 url, URL localref)
+ {
+ String codebase = localref.toString();
+ if (url.indexOf("/") == 0)
+ {
+ url = codebase.substring(0, codebase.length()
+ - localref.getFile().length())
+ + url;
+ }
+ else
+ {
+ url = localref + url;
+ }
+ return url;
+ }
+
+ /**
+ * 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) ? getDocumentBase()
+ : getCodeBase());
+ 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;
}
/**