X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=59424dfaf6ca924da90bf3a74849c2ebac1360e7;hp=c9977fd0d30d24080354498a06054b080d374aa1;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hpb=2c53eb970a6611d2d422df744044b579ef31f490
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
old mode 100755
new mode 100644
index c9977fd..59424df
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1,252 +1,1456 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
-import java.applet.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.util.*;
-
-import jalview.appletgui.*;
-import jalview.datamodel.*;
-import jalview.io.*;
+import jalview.analysis.AlignmentUtils;
+import jalview.api.StructureSelectionManagerProvider;
+import jalview.appletgui.AlignFrame;
+import jalview.appletgui.AlignViewport;
+import jalview.appletgui.EmbmenuFrame;
+import jalview.appletgui.FeatureSettings;
+import jalview.appletgui.SplitFrame;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.AnnotationFile;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.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.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;
+import java.awt.event.ActionEvent;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.URL;
+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";
- ///////////////////////////////////////////
- //The following public methods maybe called
- //externally, eg via javascript in HTML page
- /**
- * @return list of selected sequences separated by "¬"
+ public StructureSelectionManager getStructureSelectionManager()
+ {
+ return StructureSelectionManager.getStructureSelectionManager(this);
+ }
+
+ // /////////////////////////////////////////
+ // The following public methods maybe called
+ // externally, eg via javascript in HTML page
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences()
*/
public String getSelectedSequences()
{
- return getSelectedSequences(currentAlignFrame);
+ return getSelectedSequencesFrom(getDefaultTargetFrame());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
+ */
+ public String getSelectedSequences(String sep)
+ {
+ return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);
}
- public String getSelectedSequences(AlignFrame alf)
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
+ * .AlignFrame)
+ */
+ public String getSelectedSequencesFrom(AlignFrame alf)
{
- StringBuffer result = new StringBuffer("");
+ return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);
+ }
+ /*
+ * (non-Javadoc)
+ *
+ * @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 = separator; // "+0x00AC;
+ }
if (alf.viewport.getSelectionGroup() != null)
{
- SequenceI[] seqs = alf.viewport.getSelectionGroup().
- getSequencesInOrder(
- alf.viewport.getAlignment());
+ SequenceI[] seqs = alf.viewport.getSelectionGroup()
+ .getSequencesInOrder(alf.viewport.getAlignment());
for (int i = 0; i < seqs.length; i++)
{
- result.append(seqs[i].getName() + "¬");
+ result.append(seqs[i].getName());
+ result.append(sep);
}
}
return result.toString();
}
-
- public String getAlignment(String format)
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#highlight(java.lang.String,
+ * java.lang.String, java.lang.String)
+ */
+ public void highlight(String sequenceId, String position,
+ String alignedPosition)
{
- return getAlignment(currentAlignFrame, format, "true");
+ highlightIn(getDefaultTargetFrame(), sequenceId, position,
+ alignedPosition);
}
- public String getAlignment(AlignFrame alf, String format)
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#highlightIn(jalview.appletgui.AlignFrame,
+ * java.lang.String, java.lang.String, java.lang.String)
+ */
+ public void highlightIn(final AlignFrame alf, final String sequenceId,
+ final String position, final String alignedPosition)
{
- return getAlignment(alf, format, "true");
+ // TODO: could try to highlight in all alignments if alf==null
+ jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+ alf.viewport.getAlignment().getSequencesArray());
+ final SequenceI sq = matcher.findIdMatch(sequenceId);
+ if (sq != null)
+ {
+ int apos = -1;
+ try
+ {
+ apos = new Integer(position).intValue();
+ apos--;
+ } catch (NumberFormatException ex)
+ {
+ return;
+ }
+ final StructureSelectionManagerProvider me = this;
+ final int pos = apos;
+ // use vamsas listener to broadcast to all listeners in scope
+ if (alignedPosition != null
+ && (alignedPosition.trim().length() == 0 || alignedPosition
+ .toLowerCase().indexOf("false") > -1))
+ {
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ StructureSelectionManager.getStructureSelectionManager(me)
+ .mouseOverVamsasSequence(sq, sq.findIndex(pos), null);
+ }
+ });
+ }
+ else
+ {
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ StructureSelectionManager.getStructureSelectionManager(me)
+ .mouseOverVamsasSequence(sq, pos, null);
+ }
+ });
+ }
+ }
}
- public String getAlignment(String format, String suffix)
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
+ * java.lang.String)
+ */
+ public void select(String sequenceIds, String columns)
{
- return getAlignment(currentAlignFrame, format, suffix);
+ selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator);
}
- public String getAlignment(AlignFrame alf, String format, String suffix)
- {
- try
- {
- boolean seqlimits = suffix.equalsIgnoreCase("true");
- String reply = new AppletFormatAdapter().formatSequences(format,
- alf.viewport.getAlignment(), seqlimits);
- return reply;
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- return "Error retrieving alignment in " + format + " format. ";
- }
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
+ * java.lang.String, java.lang.String)
+ */
+ public void select(String sequenceIds, String columns, String sep)
+ {
+ selectIn(getDefaultTargetFrame(), sequenceIds, columns, sep);
}
- public void loadAnnotation(String annotation)
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
+ * java.lang.String, java.lang.String)
+ */
+ public void selectIn(AlignFrame alf, String sequenceIds, String columns)
{
- loadAnnotation(currentAlignFrame, annotation);
+ selectIn(alf, sequenceIds, columns, separator);
}
- public void loadAnnotation(AlignFrame alf, String annotation)
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
+ * java.lang.String, java.lang.String, java.lang.String)
+ */
+ public void selectIn(final AlignFrame alf, String sequenceIds,
+ String columns, String sep)
{
- if (new AnnotationFile().readAnnotationFile(
- alf.getAlignViewport().getAlignment(), annotation,
- AppletFormatAdapter.PASTE))
+ if (sep == null || sep.length() == 0)
{
- alf.alignPanel.fontChanged();
- alf.alignPanel.setScrollValues(0, 0);
+ sep = separator;
}
else
{
- alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
+ if (debug)
+ {
+ System.err.println("Selecting region using separator string '"
+ + separator + "'");
+ }
+ }
+ // deparse fields
+ String[] ids = separatorListToArray(sequenceIds, sep);
+ String[] cols = separatorListToArray(columns, sep);
+ final SequenceGroup sel = new SequenceGroup();
+ final ColumnSelection csel = new ColumnSelection();
+ AlignmentI al = alf.viewport.getAlignment();
+ jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+ alf.viewport.getAlignment().getSequencesArray());
+ int start = 0, end = al.getWidth(), alw = al.getWidth();
+ boolean seqsfound = true;
+ if (ids != null && ids.length > 0)
+ {
+ seqsfound = false;
+ for (int i = 0; i < ids.length; i++)
+ {
+ if (ids[i].trim().length() == 0)
+ {
+ continue;
+ }
+ SequenceI sq = matcher.findIdMatch(ids[i]);
+ if (sq != null)
+ {
+ seqsfound = true;
+ sel.addSequence(sq, false);
+ }
+ }
+ }
+ boolean inseqpos = false;
+ if (cols != null && cols.length > 0)
+ {
+ boolean seset = false;
+ for (int i = 0; i < cols.length; i++)
+ {
+ String cl = cols[i].trim();
+ if (cl.length() == 0)
+ {
+ continue;
+ }
+ int p;
+ if ((p = cl.indexOf("-")) > -1)
+ {
+ int from = -1, to = -1;
+ try
+ {
+ from = new Integer(cl.substring(0, p)).intValue();
+ from--;
+ } catch (NumberFormatException ex)
+ {
+ System.err
+ .println("ERROR: Couldn't parse first integer in range element column selection string '"
+ + cl + "' - format is 'from-to'");
+ return;
+ }
+ try
+ {
+ to = new Integer(cl.substring(p + 1)).intValue();
+ to--;
+ } catch (NumberFormatException ex)
+ {
+ System.err
+ .println("ERROR: Couldn't parse second integer in range element column selection string '"
+ + cl + "' - format is 'from-to'");
+ return;
+ }
+ if (from >= 0 && to >= 0)
+ {
+ // valid range
+ if (from < to)
+ {
+ int t = to;
+ to = from;
+ to = t;
+ }
+ if (!seset)
+ {
+ start = from;
+ end = to;
+ seset = true;
+ }
+ else
+ {
+ // comment to prevent range extension
+ if (start > from)
+ {
+ start = from;
+ }
+ if (end < to)
+ {
+ end = to;
+ }
+ }
+ for (int r = from; r <= to; r++)
+ {
+ if (r >= 0 && r < alw)
+ {
+ csel.addElement(r);
+ }
+ }
+ if (debug)
+ {
+ System.err.println("Range '" + cl + "' deparsed as [" + from
+ + "," + to + "]");
+ }
+ }
+ else
+ {
+ System.err.println("ERROR: Invalid Range '" + cl
+ + "' deparsed as [" + from + "," + to + "]");
+ }
+ }
+ else
+ {
+ int r = -1;
+ try
+ {
+ r = new Integer(cl).intValue();
+ r--;
+ } catch (NumberFormatException ex)
+ {
+ if (cl.toLowerCase().equals("sequence"))
+ {
+ // we are in the dataset sequence's coordinate frame.
+ inseqpos = true;
+ }
+ else
+ {
+ System.err
+ .println("ERROR: Couldn't parse integer from point selection element of column selection string '"
+ + cl + "'");
+ return;
+ }
+ }
+ if (r >= 0 && r <= alw)
+ {
+ if (!seset)
+ {
+ start = r;
+ end = r;
+ seset = true;
+ }
+ else
+ {
+ // comment to prevent range extension
+ if (start > r)
+ {
+ start = r;
+ }
+ if (end < r)
+ {
+ end = r;
+ }
+ }
+ csel.addElement(r);
+ if (debug)
+ {
+ System.err.println("Point selection '" + cl
+ + "' deparsed as [" + r + "]");
+ }
+ }
+ else
+ {
+ System.err.println("ERROR: Invalid Point selection '" + cl
+ + "' deparsed as [" + r + "]");
+ }
+ }
+ }
+ }
+ if (seqsfound)
+ {
+ // we only propagate the selection when it was the null selection, or the
+ // given sequences were found in the alignment.
+ if (inseqpos && sel.getSize() > 0)
+ {
+ // assume first sequence provides reference frame ?
+ SequenceI rs = sel.getSequenceAt(0);
+ start = rs.findIndex(start);
+ end = rs.findIndex(end);
+ if (csel != null)
+ {
+ List cs = 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);
+ }
+ });
}
}
- public String getFeatures(String format)
- {
- return getFeatures(currentAlignFrame, format);
- }
- public String getFeatures(AlignFrame alf, String format)
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignment(java.lang.
+ * String, java.lang.String)
+ */
+ public String getSelectedSequencesAsAlignment(String format, String suffix)
{
- return alf.outputFeatures(false, format);
+ return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(),
+ format, suffix);
}
- public String getAnnotation()
+
+ /*
+ * (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)
{
- return getAnnotation(currentAlignFrame);
+ try
+ {
+ 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 reply;
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ return "Error retrieving alignment in " + format + " format. ";
+ }
+ return "";
}
- public String getAnnotation(AlignFrame alf)
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder()
+ */
+ public String getAlignmentOrder()
{
- return alf.outputAnnotations(false);
+ return getAlignmentOrderFrom(getDefaultTargetFrame());
}
- public AlignFrame newView()
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
+ * )
+ */
+ public String getAlignmentOrderFrom(AlignFrame alf)
{
- return newView(currentAlignFrame);
+ return getAlignmentOrderFrom(alf, separator);
}
- public AlignFrame newView(String name)
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
+ * , java.lang.String)
+ */
+ public String getAlignmentOrderFrom(AlignFrame alf, String sep)
{
- return newView(currentAlignFrame, name);
+ 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);
}
- public AlignFrame newView(AlignFrame alf)
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
+ * java.lang.String)
+ */
+ public String orderBy(String order, String undoName)
{
- return alf.newView(null);
+ return orderBy(order, undoName, separator);
}
- public AlignFrame newView(AlignFrame alf, String name)
+
+ /*
+ * (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 alf.newView(name);
+ return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep);
}
- /**
+
+ /*
+ * (non-Javadoc)
*
- * @param text alignment file as a string
- * @param title window title
- * @return null or new alignment frame
+ * @see
+ * jalview.bin.JalviewLiteJsApi#orderAlignmentBy(jalview.appletgui.AlignFrame,
+ * java.lang.String, java.lang.String, java.lang.String)
*/
- public AlignFrame loadAlignment(String text, String title)
+ public String orderAlignmentBy(AlignFrame alf, String order,
+ String undoName, String sep)
{
- Alignment al = null;
- String format = new IdentifyFile().Identify(text, AppletFormatAdapter.PASTE);
- try
+ String[] ids = separatorListToArray(order, sep);
+ SequenceI[] sqs = null;
+ if (ids != null && ids.length > 0)
{
- al = new AppletFormatAdapter().readFile(text,
- AppletFormatAdapter.PASTE,
- format);
- if (al.getHeight() > 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++)
{
- return new AlignFrame(al, this, title, false);
+ 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;
}
}
- catch (java.io.IOException ex)
+ if (sqs == null)
{
- ex.printStackTrace();
+ return "";
}
- return null;
- }
-
- ////////////////////////////////////////////////
- ////////////////////////////////////////////////
-
-
-
- static int lastFrameX = 200;
- static int lastFrameY = 200;
- boolean fileFound = true;
- String file = "No file";
- Button launcher = new Button("Start Jalview");
+ ;
+ final AlignmentOrder aorder = new AlignmentOrder(sqs);
- //The currentAlignFrame is static, it will change
- //if and when the user selects a new window
- public static AlignFrame currentAlignFrame;
+ 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 : "";
+ }
- //This is the first frame to be displayed, and does not change
- AlignFrame initialAlignFrame;
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String)
+ */
+ public String getAlignment(String format)
+ {
+ return getAlignmentFrom(getDefaultTargetFrame(), format, TRUE);
+ }
- boolean embedded = false;
+ /*
+ * (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);
+ }
- public boolean jmolAvailable = false;
- public static boolean debug;
+ /*
+ * (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);
+ }
- /**
- * init method for Jalview Applet
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
+ * java.lang.String, java.lang.String)
*/
- public void init()
+ public String getAlignmentFrom(AlignFrame alf, String format,
+ String suffix)
{
- String dbg = getParameter("debug");
- if (dbg!=null)
+ try
{
- debug = dbg.toLowerCase().equals("true");
- }
- int r = 255;
- int g = 255;
- int b = 255;
- String param = getParameter("RGB");
+ boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
- if (param != null)
+ String reply = new AppletFormatAdapter().formatSequences(format,
+ alf.viewport.getAlignment(), seqlimits);
+ return reply;
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ return "Error retrieving alignment in " + format + " format. ";
+ }
+ }
+
+ /*
+ * (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().annotateAlignmentView(alf.getAlignViewport(),
+ annotation, AppletFormatAdapter.PASTE))
+ {
+ alf.alignPanel.fontChanged();
+ alf.alignPanel.setScrollValues(0, 0);
+ }
+ else
+ {
+ alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
+ }
+ }
+
+ /*
+ * (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)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String,
+ * java.lang.String)
+ */
+ public AlignFrame loadAlignment(String text, String title)
+ {
+ AlignmentI al = null;
+
+ String format = new IdentifyFile().Identify(text,
+ AppletFormatAdapter.PASTE);
+ try
+ {
+ al = new AppletFormatAdapter().readFile(text,
+ AppletFormatAdapter.PASTE, format);
+ if (al.getHeight() > 0)
+ {
+ return new AlignFrame(al, this, title, false);
+ }
+ } catch (java.io.IOException ex)
+ {
+ ex.printStackTrace();
+ }
+ return null;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String)
+ */
+ public void setMouseoverListener(String listener)
+ {
+ setMouseoverListener(currentAlignFrame, listener);
+ }
+
+ private Vector javascriptListeners = new Vector();
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame
+ * , java.lang.String)
+ */
+ public void setMouseoverListener(AlignFrame af, String listener)
+ {
+ if (listener != null)
+ {
+ listener = listener.trim();
+ if (listener.length() == 0)
+ {
+ System.err
+ .println("jalview Javascript error: Ignoring empty function for mouseover listener.");
+ return;
+ }
+ }
+ jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener(
+ this, af, listener);
+ javascriptListeners.addElement(mol);
+ StructureSelectionManager.getStructureSelectionManager(this)
+ .addStructureViewerListener(mol);
+ if (debug)
+ {
+ System.err.println("Added a mouseover listener for "
+ + ((af == null) ? "All frames" : "Just views for "
+ + af.getAlignViewport().getSequenceSetId()));
+ System.err.println("There are now " + javascriptListeners.size()
+ + " listeners in total.");
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String)
+ */
+ 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)
+ {
+ listener = listener.trim();
+ if (listener.length() == 0)
+ {
+ System.err
+ .println("jalview Javascript error: Ignoring empty function for selection listener.");
+ return;
+ }
+ }
+ jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender(
+ this, af, listener);
+ javascriptListeners.addElement(mol);
+ StructureSelectionManager.getStructureSelectionManager(this)
+ .addSelectionListener(mol);
+ if (debug)
+ {
+ System.err.println("Added a selection listener for "
+ + ((af == null) ? "All frames" : "Just views for "
+ + af.getAlignViewport().getSequenceSetId()));
+ System.err.println("There are now " + javascriptListeners.size()
+ + " listeners in total.");
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @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)
+ {
+ if (listener != null)
+ {
+ listener = listener.trim();
+ if (listener.length() == 0)
+ {
+ listener = null;
+ }
+ }
+ boolean rprt = false;
+ for (int ms = 0, msSize = javascriptListeners.size(); ms < msSize;)
+ {
+ Object lstn = javascriptListeners.elementAt(ms);
+ JsCallBack lstner = (JsCallBack) lstn;
+ if ((af == null || lstner.getAlignFrame() == af)
+ && (listener == null || lstner.getListenerFunction().equals(
+ listener)))
+ {
+ javascriptListeners.removeElement(lstner);
+ msSize--;
+ if (lstner instanceof SelectionListener)
+ {
+ StructureSelectionManager.getStructureSelectionManager(this)
+ .removeSelectionListener((SelectionListener) lstner);
+ }
+ else
+ {
+ StructureSelectionManager.getStructureSelectionManager(this)
+ .removeStructureViewerListener(lstner, null);
+ }
+ rprt = debug;
+ if (debug)
+ {
+ System.err.println("Removed listener '" + listener + "'");
+ }
+ }
+ else
+ {
+ ms++;
+ }
+ }
+ if (rprt)
+ {
+ System.err.println("There are now " + javascriptListeners.size()
+ + " listeners in total.");
+ }
+ }
+
+ public void stop()
+ {
+ System.err.println("Applet " + getName() + " stop().");
+ tidyUp();
+ }
+
+ public void destroy()
+ {
+ System.err.println("Applet " + getName() + " destroy().");
+ tidyUp();
+ }
+
+ private void tidyUp()
+ {
+ removeAll();
+ if (currentAlignFrame != null && currentAlignFrame.viewport != null
+ && currentAlignFrame.viewport.applet != null)
+ {
+ AlignViewport av = currentAlignFrame.viewport;
+ currentAlignFrame.closeMenuItem_actionPerformed();
+ av.applet = null;
+ currentAlignFrame = null;
+ }
+ if (javascriptListeners != null)
+ {
+ while (javascriptListeners.size() > 0)
+ {
+ jalview.javascript.JSFunctionExec mol = javascriptListeners
+ .elementAt(0);
+ javascriptListeners.removeElement(mol);
+ if (mol instanceof SelectionListener)
+ {
+ StructureSelectionManager.getStructureSelectionManager(this)
+ .removeSelectionListener((SelectionListener) mol);
+ }
+ else
+ {
+ StructureSelectionManager.getStructureSelectionManager(this)
+ .removeStructureViewerListener(mol, null);
+ }
+ mol.jvlite = null;
+ }
+ }
+ if (jsFunctionExec != null)
+ {
+ jsFunctionExec.stopQueue();
+ jsFunctionExec.jvlite = null;
+ }
+ initialAlignFrame = null;
+ jsFunctionExec = null;
+ javascriptListeners = null;
+ StructureSelectionManager.release(this);
+ }
+
+ private jalview.javascript.JSFunctionExec jsFunctionExec;
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String,
+ * java.lang.String, java.lang.String)
+ */
+ public void mouseOverStructure(final String pdbResNum,
+ final String chain, final String pdbfile)
+ {
+ final StructureSelectionManagerProvider me = this;
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ try
+ {
+ StructureSelectionManager.getStructureSelectionManager(me)
+ .mouseOverStructure(new Integer(pdbResNum).intValue(),
+ chain, pdbfile);
+ if (debug)
+ {
+ System.err.println("mouseOver for '" + pdbResNum
+ + "' in chain '" + chain + "' in structure '" + pdbfile
+ + "'");
+ }
+ } catch (NumberFormatException e)
+ {
+ System.err.println("Ignoring invalid residue number string '"
+ + pdbResNum + "'");
+ }
+
+ }
+ });
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#scrollViewToIn(jalview.appletgui.AlignFrame,
+ * java.lang.String, java.lang.String)
+ */
+ 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();
+ }
+ }
+ });
+
+ }
+
+ // //////////////////////////////////////////////
+ // //////////////////////////////////////////////
+
+ public static int lastFrameX = 200;
+
+ public static int lastFrameY = 200;
+
+ boolean fileFound = true;
+
+ String file = "No file";
+
+ String file2 = null;
+
+ Button launcher = new Button(
+ MessageManager.getString("label.start_jalview"));
+
+ /**
+ * The currentAlignFrame is static, it will change if and when the user
+ * selects a new window. Note that it will *never* point back to the embedded
+ * AlignFrame if the applet is started as embedded on the page and then
+ * afterwards a new view is created.
+ */
+ public AlignFrame currentAlignFrame = null;
+
+ /**
+ * This is the first frame to be displayed, and does not change. API calls
+ * will default to this instance if currentAlignFrame is null.
+ */
+ AlignFrame initialAlignFrame = null;
+
+ boolean embedded = false;
+
+ private boolean checkForJmol = true;
+
+ private boolean checkedForJmol = false; // ensure we don't check for jmol
+
+ // every time the app is re-inited
+
+ public boolean jmolAvailable = false;
+
+ private boolean alignPdbStructures = false;
+
+ /**
+ * use an external structure viewer exclusively (no jmols or MCViews will be
+ * opened by JalviewLite itself)
+ */
+ public boolean useXtrnalSviewer = false;
+
+ public static boolean debug = false;
+
+ static String builddate = null, version = null, installation = null;
+
+ private static void initBuildDetails()
+ {
+ if (builddate == null)
+ {
+ builddate = "unknown";
+ version = "test";
+ installation = "applet";
+ java.net.URL url = JalviewLite.class
+ .getResource("/.build_properties");
+ if (url != null)
+ {
+ try
+ {
+ BufferedReader reader = new BufferedReader(new InputStreamReader(
+ url.openStream()));
+ String line;
+ while ((line = reader.readLine()) != null)
+ {
+ if (line.indexOf("VERSION") > -1)
+ {
+ version = line.substring(line.indexOf("=") + 1);
+ }
+ if (line.indexOf("BUILD_DATE") > -1)
+ {
+ builddate = line.substring(line.indexOf("=") + 1);
+ }
+ if (line.indexOf("INSTALLATION") > -1)
+ {
+ installation = line.substring(line.indexOf("=") + 1);
+ }
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ }
+ }
+
+ public static String getBuildDate()
+ {
+ initBuildDetails();
+ return builddate;
+ }
+
+ public static String getInstallation()
+ {
+ initBuildDetails();
+ return installation;
+ }
+
+ public static String getVersion()
+ {
+ initBuildDetails();
+ return version;
+ }
+
+ // public JSObject scriptObject = null;
+
+ /**
+ * init method for Jalview Applet
+ */
+ 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
+ */
+ debug = TRUE.equalsIgnoreCase(getParameter("debug"));
+ if (debug)
+ {
+
+ System.err.println("JalviewLite Version " + getVersion());
+ System.err.println("Build Date : " + getBuildDate());
+ System.err.println("Installation : " + getInstallation());
+
+ }
+ String externalsviewer = getParameter("externalstructureviewer");
+ if (externalsviewer != null)
+ {
+ useXtrnalSviewer = externalsviewer.trim().toLowerCase().equals(TRUE);
+ }
+ /**
+ * if true disable the check for jmol
+ */
+ String chkforJmol = getParameter("nojmol");
+ if (chkforJmol != null)
+ {
+ checkForJmol = !chkforJmol.equals(TRUE);
+ }
+ /**
+ * get the separator parameter if present
+ */
+ String sep = getParameter("separator");
+ if (sep != null)
+ {
+ if (sep.length() > 0)
+ {
+ separator = sep;
+ if (debug)
+ {
+ System.err.println("Separator set to '" + separator + "'");
+ }
+ }
+ else
+ {
+ throw new Error(
+ MessageManager
+ .getString("error.invalid_separator_parameter"));
+ }
+ }
+ int r = 255;
+ int g = 255;
+ int b = 255;
+ String param = getParameter("RGB");
+
+ if (param != null)
{
try
{
r = Integer.parseInt(param.substring(0, 2), 16);
g = Integer.parseInt(param.substring(2, 4), 16);
b = Integer.parseInt(param.substring(4, 6), 16);
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
r = 255;
g = 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");
if (file == null)
{
- //Maybe the sequences are added as parameters
+ // Maybe the sequences are added as parameters
StringBuffer data = new StringBuffer("PASTE");
int i = 1;
- while ( (file = getParameter("sequence" + i)) != null)
+ while ((file = getParameter("sequence" + i)) != null)
{
data.append(file.toString() + "\n");
i++;
@@ -256,50 +1460,146 @@ public class JalviewLite
file = data.toString();
}
}
+ if (getDefaultParameter("enableSplitFrame", true))
+ {
+ file2 = getParameter("file2");
+ }
+
+ embedded = TRUE.equalsIgnoreCase(getParameter("embedded"));
+ if (embedded)
+ {
+ LoadingThread loader = new LoadingThread(file, file2, this);
+ loader.start();
+ }
+ else if (file != null)
+ {
+ /*
+ * Start the applet immediately or show a button to start it
+ */
+ if (FALSE.equalsIgnoreCase(getParameter("showbutton")))
+ {
+ LoadingThread loader = new LoadingThread(file, file2, this);
+ loader.start();
+ }
+ else
+ {
+ add(launcher);
+ launcher.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ LoadingThread loader = new LoadingThread(file, file2,
+ JalviewLite.this);
+ loader.start();
+ }
+ });
+ }
+ }
+ else
+ {
+ // jalview initialisation with no alignment. loadAlignment() method can
+ // still be called to open new alignments.
+ file = "NO FILE";
+ fileFound = false;
+ callInitCallback();
+ }
+ }
- LoadJmolThread jmolAvailable = new LoadJmolThread();
- jmolAvailable.start();
+ private void initLiveConnect()
+ {
+ // try really hard to get the liveConnect thing working
+ boolean notFailed = false;
+ int tries = 0;
+ while (!notFailed && tries < 10)
+ {
+ if (tries > 0)
+ {
+ System.err.println("LiveConnect request thread going to sleep.");
+ }
+ try
+ {
+ Thread.sleep(700 * (1 + tries));
+ } catch (InterruptedException q)
+ {
+ }
+ ;
+ if (tries++ > 0)
+ {
+ System.err.println("LiveConnect request thread woken up.");
+ }
+ try
+ {
+ JSObject scriptObject = JSObject.getWindow(this);
+ if (scriptObject.eval("navigator") != null)
+ {
+ notFailed = true;
+ }
+ } catch (Exception jsex)
+ {
+ System.err.println("Attempt " + tries
+ + " to access LiveConnect javascript failed.");
+ }
+ }
+ }
- final JalviewLite applet = this;
- if (getParameter("embedded") != null
- && getParameter("embedded").equalsIgnoreCase("true"))
+ private void callInitCallback()
+ {
+ String initjscallback = getParameter("oninit");
+ if (initjscallback == null)
{
- embedded = true;
- LoadingThread loader = new LoadingThread(file, applet);
- loader.start();
+ return;
}
- else if (file != null)
+ initjscallback = initjscallback.trim();
+ if (initjscallback.length() > 0)
{
- add(launcher);
+ JSObject scriptObject = null;
+ try
+ {
+ scriptObject = JSObject.getWindow(this);
+ } catch (Exception ex)
+ {
+ }
+ ;
+ // try really hard to let the browser plugin know we want liveconnect
+ initLiveConnect();
- launcher.addActionListener(new java.awt.event.ActionListener()
+ if (scriptObject != null)
{
- public void actionPerformed(ActionEvent e)
+ try
+ {
+ // do onInit with the JS executor thread
+ new JSFunctionExec(this).executeJavascriptFunction(true,
+ initjscallback, null, "Calling oninit callback '"
+ + initjscallback + "'.");
+ } catch (Exception e)
{
- LoadingThread loader = new LoadingThread(file,
- applet);
- loader.start();
+ System.err.println("Exception when executing _oninit callback '"
+ + initjscallback + "'.");
+ e.printStackTrace();
}
- });
- }
- else
- {
- file = "NO FILE";
- fileFound = false;
+ }
+ else
+ {
+ System.err.println("Not executing _oninit callback '"
+ + initjscallback + "' - no scripting allowed.");
+ }
}
}
-
/**
* Initialises and displays a new java.awt.Frame
- *
- * @param frame java.awt.Frame to be displayed
- * @param title title of new frame
- * @param width width if new frame
- * @param height height of new frame
+ *
+ * @param frame
+ * java.awt.Frame to be displayed
+ * @param title
+ * title of new frame
+ * @param width
+ * width if new frame
+ * @param height
+ * height of new frame
*/
public static void addFrame(final Frame frame, String title, int width,
- int height)
+ int height)
{
frame.setLocation(lastFrameX, lastFrameY);
lastFrameX += 40;
@@ -312,14 +1612,22 @@ public class JalviewLite
{
if (frame instanceof AlignFrame)
{
- ( (AlignFrame) frame).closeMenuItem_actionPerformed();
- }
- if (currentAlignFrame == frame)
- {
- currentAlignFrame = null;
+ AlignViewport vp = ((AlignFrame) frame).viewport;
+ ((AlignFrame) frame).closeMenuItem_actionPerformed();
+ if (vp.applet.currentAlignFrame == frame)
+ {
+ vp.applet.currentAlignFrame = null;
+ }
+ vp.applet = null;
+ vp = null;
+
}
lastFrameX -= 40;
lastFrameY -= 40;
+ if (frame instanceof EmbmenuFrame)
+ {
+ ((EmbmenuFrame) frame).destroyMenus();
+ }
frame.setMenuBar(null);
frame.dispose();
}
@@ -328,24 +1636,38 @@ public class JalviewLite
{
if (frame instanceof AlignFrame)
{
- currentAlignFrame = (AlignFrame) frame;
+ ((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame;
if (debug)
{
- System.err.println("Activated window "+frame);
+ System.err.println("Activated window " + frame);
}
}
+ // be good.
+ super.windowActivated(e);
}
-
+ /*
+ * Probably not necessary to do this - see TODO above. (non-Javadoc)
+ *
+ * @see
+ * java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent
+ * )
+ *
+ * public void windowDeactivated(WindowEvent e) { if (currentAlignFrame ==
+ * frame) { currentAlignFrame = null; if (debug) {
+ * System.err.println("Deactivated window "+frame); } }
+ * super.windowDeactivated(e); }
+ */
});
frame.setVisible(true);
}
/**
- * This paints the background surrounding the "Launch Jalview button"
+ * This paints the background surrounding the "Launch Jalview button"
*
- *
If file given in parameter not found, displays error message
- *
- * @param g graphics context
+ * If file given in parameter not found, displays error message
+ *
+ * @param g
+ * graphics context
*/
public void paint(Graphics g)
{
@@ -355,55 +1677,123 @@ public class JalviewLite
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;
+
public void run()
{
- try
+ if (running || checkedForJmol)
+ {
+ return;
+ }
+ running = true;
+ if (checkForJmol)
{
- if (!System.getProperty("java.version").startsWith("1.1"))
+ try
+ {
+ if (!System.getProperty("java.version").startsWith("1.1"))
+ {
+ Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
+ jmolAvailable = true;
+ }
+ if (!jmolAvailable)
+ {
+ System.out
+ .println("Jmol not available - Using MCview for structures");
+ }
+ } catch (java.lang.ClassNotFoundException ex)
{
- Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
- jmolAvailable = true;
}
}
- catch (java.lang.ClassNotFoundException ex)
+ else
{
- System.out.println("Jmol not available - Using MCview for structures");
+ jmolAvailable = false;
+ if (debug)
+ {
+ System.err
+ .println("Skipping Jmol check. Will use MCView (probably)");
+ }
}
+ checkedForJmol = true;
+ running = false;
}
- }
+ public boolean notFinished()
+ {
+ return running || !checkedForJmol;
+ }
+ }
- class LoadingThread
- extends Thread
+ class LoadingThread extends Thread
{
- String file;
+ /**
+ * State variable: protocol for access to file source
+ */
String protocol;
- String format;
+
+ String _file; // alignment file or URL spec
+
+ String _file2; // second alignment file or URL spec
+
JalviewLite applet;
- public LoadingThread(String _file,
- JalviewLite _applet)
+ private void dbgMsg(String msg)
{
- if (applet.debug)
+ if (JalviewLite.debug)
{
- System.err.println("Loading thread started with:\n>>file\n"+_file+">>endfile");
+ System.err.println(msg);
}
- file = _file;
+ }
+
+ /**
+ * update the protocol state variable for accessing the datasource located
+ * by file.
+ *
+ * @param file
+ * @return possibly updated datasource string
+ */
+ public String setProtocolState(String file)
+ {
if (file.startsWith("PASTE"))
{
file = file.substring(5);
@@ -418,407 +1808,1194 @@ public class JalviewLite
file = addProtocol(file);
protocol = AppletFormatAdapter.URL;
}
- if (applet.debug)
- {
- System.err.println("Protocol identified as '"+protocol+"'");
- }
- format = new jalview.io.IdentifyFile().Identify(file, protocol);
- if (applet.debug)
- {
- System.err.println("File identified as '"+format+"'");
- }
+ dbgMsg("Protocol identified as '" + protocol + "'");
+ return file;
+ }
+
+ public LoadingThread(String file, String file2, JalviewLite _applet)
+ {
+ this._file = file;
+ this._file2 = file2;
applet = _applet;
}
public void run()
{
+ LoadJmolThread jmolchecker = new LoadJmolThread();
+ jmolchecker.start();
+ while (jmolchecker.notFinished())
+ {
+ // wait around until the Jmol check is complete.
+ try
+ {
+ Thread.sleep(2);
+ } catch (Exception e)
+ {
+ }
+ }
startLoading();
+ // applet.callInitCallback();
}
+ /**
+ * Load the alignment and any related files as specified by applet
+ * parameters
+ */
private void startLoading()
{
- Alignment al = null;
- try
+ dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");
+
+ dbgMsg("Loading started.");
+
+ AlignFrame newAlignFrame = readAlignment(_file);
+ AlignFrame newAlignFrame2 = readAlignment(_file2);
+ if (newAlignFrame != null)
{
- al = new AppletFormatAdapter().readFile(file, protocol,
- format);
+ addToDisplay(newAlignFrame, newAlignFrame2);
+ loadTree(newAlignFrame);
+
+ loadScoreFile(newAlignFrame);
+
+ loadFeatures(newAlignFrame);
+
+ loadAnnotations(newAlignFrame);
+
+ loadJnetFile(newAlignFrame);
+
+ loadPdbFiles(newAlignFrame);
}
- catch (java.io.IOException ex)
+ else
{
- ex.printStackTrace();
+ fileFound = false;
+ applet.remove(launcher);
+ applet.repaint();
}
- if ( (al != null) && (al.getHeight() > 0))
- {
- currentAlignFrame = new AlignFrame(al,
- applet,
- file,
- embedded);
+ callInitCallback();
+ }
- if (protocol == jalview.io.AppletFormatAdapter.PASTE)
+ /**
+ * 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();
+ if (AlignmentUtils.isMappable(al1, al2))
{
- currentAlignFrame.setTitle("Sequences from " + getDocumentBase());
+ SplitFrame sf = new SplitFrame(af, af2);
+ sf.addToDisplay(embedded, JalviewLite.this);
+ return;
}
-
- initialAlignFrame = currentAlignFrame;
-
- currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
-
- String treeFile = applet.getParameter("tree");
- if (treeFile == null)
+ else
{
- treeFile = applet.getParameter("treeFile");
+ 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);
+ }
- if (treeFile != null)
+ /**
+ * Read the alignment file (from URL, text 'paste', or archive by
+ * classloader).
+ *
+ * @return
+ */
+ protected AlignFrame readAlignment(String fileParam)
+ {
+ if (fileParam == null)
+ {
+ return null;
+ }
+ String resolvedFile = setProtocolState(fileParam);
+ String format = new IdentifyFile().Identify(resolvedFile, protocol);
+ dbgMsg("File identified as '" + format + "'");
+ AlignmentI al = null;
+ try
+ {
+ al = new AppletFormatAdapter().readFile(resolvedFile, protocol,
+ format);
+ if ((al != null) && (al.getHeight() > 0))
{
- try
+ dbgMsg("Successfully loaded file.");
+ al.setDataset(null);
+ AlignFrame newAlignFrame = new AlignFrame(al, applet,
+ resolvedFile, embedded, false);
+ newAlignFrame.setTitle(resolvedFile);
+ if (initialAlignFrame == null)
{
- if (inArchive(treeFile))
- {
- protocol = AppletFormatAdapter.CLASSLOADER;
- }
- else
- {
- protocol = AppletFormatAdapter.URL;
- treeFile = addProtocol(treeFile);
- }
+ initialAlignFrame = newAlignFrame;
+ }
+ // update the focus.
+ currentAlignFrame = newAlignFrame;
- jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile,
- protocol);
+ if (protocol == AppletFormatAdapter.PASTE)
+ {
+ newAlignFrame.setTitle(MessageManager.formatMessage(
+ "label.sequences_from", new Object[] { applet
+ .getDocumentBase().toString() }));
+ }
- fin.parse();
+ newAlignFrame.statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_loaded_file",
+ new Object[] { resolvedFile }));
- if (fin.getTree() != null)
+ return newAlignFrame;
+ }
+ } catch (java.io.IOException ex)
+ {
+ dbgMsg("File load exception.");
+ ex.printStackTrace();
+ if (debug)
+ {
+ try
+ {
+ FileParse fp = new FileParse(resolvedFile, protocol);
+ String ln = null;
+ dbgMsg(">>>Dumping contents of '" + resolvedFile + "' " + "("
+ + protocol + ")");
+ while ((ln = fp.nextLine()) != null)
{
- currentAlignFrame.loadTree(fin, treeFile);
+ dbgMsg(ln);
}
- }
- catch (Exception ex)
+ dbgMsg(">>>Dump finished.");
+ } catch (Exception e)
{
- ex.printStackTrace();
+ System.err
+ .println("Exception when trying to dump the content of the file parameter.");
+ e.printStackTrace();
}
}
+ }
+ return null;
+ }
- String param = getParameter("features");
- if (param != null)
+ /**
+ * Load PDBFiles if any specified by parameter(s). Returns true if loaded,
+ * else false.
+ *
+ * @param alignFrame
+ * @return
+ */
+ protected boolean loadPdbFiles(AlignFrame alignFrame)
+ {
+ boolean result = false;
+ /*
+ * Undocumented for 2.6 -
+ * related to JAL-434
+ */
+
+ applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",
+ false));
+ /*
+ *
+ *
+ *
+ *
+ *
+ */
+
+ int pdbFileCount = 0;
+ // Accumulate pdbs here if they are heading for the same view (if
+ // alignPdbStructures is true)
+ Vector pdbs = new Vector();
+ // create a lazy matcher if we're asked to
+ jalview.analysis.SequenceIdMatcher matcher = (applet
+ .getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher(
+ alignFrame.getAlignViewport().getAlignment()
+ .getSequencesArray()) : null;
+
+ String param;
+ do
+ {
+ if (pdbFileCount > 0)
{
- if (!inArchive(param))
- {
- param = addProtocol(param);
- }
-
- currentAlignFrame.parseFeaturesFile(param, protocol);
+ param = applet.getParameter("PDBFILE" + pdbFileCount);
}
-
- param = getParameter("showFeatureSettings");
- if (param != null && param.equalsIgnoreCase("true"))
+ else
{
- currentAlignFrame.viewport.showSequenceFeatures(true);
- new FeatureSettings(currentAlignFrame.alignPanel);
+ param = applet.getParameter("PDBFILE");
}
- param = getParameter("annotations");
if (param != null)
{
- if (!inArchive(param))
- {
- param = addProtocol(param);
- }
+ PDBEntry pdb = new PDBEntry();
- new AnnotationFile().readAnnotationFile(
- currentAlignFrame.viewport.getAlignment(),
- param,
- protocol);
+ String seqstring;
+ SequenceI[] seqs = null;
+ String[] chains = null;
- currentAlignFrame.alignPanel.fontChanged();
- currentAlignFrame.alignPanel.setScrollValues(0, 0);
-
- }
+ StringTokenizer st = new StringTokenizer(param, " ");
- param = getParameter("jnetfile");
- if (param != null)
- {
- try
+ if (st.countTokens() < 2)
{
- if (inArchive(param))
- {
- protocol = AppletFormatAdapter.CLASSLOADER;
- }
- else
+ String sequence = applet.getParameter("PDBSEQ");
+ if (sequence != null)
{
- protocol = AppletFormatAdapter.URL;
- param = addProtocol(param);
+ seqs = new SequenceI[] { matcher == null ? (Sequence) alignFrame
+ .getAlignViewport().getAlignment().findName(sequence)
+ : matcher.findIdMatch(sequence) };
}
- jalview.io.JPredFile predictions = new jalview.io.JPredFile(
- param, protocol);
- new JnetAnnotationMaker().add_annotation(predictions,
- currentAlignFrame.viewport.getAlignment(),
- 0, false); // do not add sequence profile from concise output
- currentAlignFrame.alignPanel.fontChanged();
- currentAlignFrame.alignPanel.setScrollValues(0, 0);
}
- catch (Exception ex)
+ else
{
- ex.printStackTrace();
- }
- }
-
- /*
-
-
-
-
-
- */
+ param = st.nextToken();
+ Vector tmp = new Vector();
+ Vector tmp2 = new Vector();
+ while (st.hasMoreTokens())
+ {
+ seqstring = st.nextToken();
+ StringTokenizer st2 = new StringTokenizer(seqstring, "=");
+ if (st2.countTokens() > 1)
+ {
+ // This is the chain
+ tmp2.addElement(st2.nextToken());
+ seqstring = st2.nextToken();
+ }
+ tmp.addElement(matcher == null ? (Sequence) alignFrame
+ .getAlignViewport().getAlignment()
+ .findName(seqstring) : matcher.findIdMatch(seqstring));
+ }
- int pdbFileCount = 0;
- do{
- if (pdbFileCount > 0)
- param = getParameter("PDBFILE" + pdbFileCount);
- else
- param = getParameter("PDBFILE");
+ seqs = new SequenceI[tmp.size()];
+ tmp.copyInto(seqs);
+ if (tmp2.size() == tmp.size())
+ {
+ chains = new String[tmp2.size()];
+ tmp2.copyInto(chains);
+ }
+ }
+ param = setProtocolState(param);
- if (param != null)
+ if (// !jmolAvailable
+ // &&
+ protocol == AppletFormatAdapter.CLASSLOADER && !useXtrnalSviewer)
{
- PDBEntry pdb = new PDBEntry();
-
- String seqstring;
- SequenceI[] seqs = null;
- String [] chains = null;
-
- StringTokenizer st = new StringTokenizer(param, " ");
+ // 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
+ // the local pdb file was identified in the class loader
+ protocol = AppletFormatAdapter.URL; // this is probably NOT
+ // CORRECT!
+ param = addProtocol(param); //
+ }
- if (st.countTokens() < 2)
- {
- String sequence = applet.getParameter("PDBSEQ");
- if (sequence != null)
- seqs = new SequenceI[]
- {
- (Sequence) currentAlignFrame.
- getAlignViewport().getAlignment().
- findName(sequence)};
+ pdb.setFile(param);
- }
- else
+ if (seqs != null)
+ {
+ for (int i = 0; i < seqs.length; i++)
{
- param = st.nextToken();
- Vector tmp = new Vector();
- Vector tmp2 = new Vector();
-
- while (st.hasMoreTokens())
+ if (seqs[i] != null)
{
- seqstring = st.nextToken();
- StringTokenizer st2 = new StringTokenizer(seqstring,"=");
- if(st2.countTokens()>1)
- {
- //This is the chain
- tmp2.addElement(st2.nextToken());
- seqstring = st2.nextToken();
- }
- tmp.addElement( (Sequence) currentAlignFrame.
- getAlignViewport().getAlignment().
- findName(seqstring));
+ ((Sequence) seqs[i]).addPDBId(pdb);
+ StructureSelectionManager.getStructureSelectionManager(
+ applet).registerPDBEntry(pdb);
}
-
- seqs = new SequenceI[tmp.size()];
- tmp.copyInto(seqs);
- if(tmp2.size()==tmp.size())
+ else
{
- chains = new String[tmp2.size()];
- tmp2.copyInto(chains);
+ 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 (inArchive(param) && !jmolAvailable)
+ if (!alignPdbStructures)
{
- protocol = AppletFormatAdapter.CLASSLOADER;
+ alignFrame.newStructureView(applet, pdb, seqs, chains,
+ protocol);
}
else
{
- protocol = AppletFormatAdapter.URL;
- param = addProtocol(param);
+ pdbs.addElement(new Object[] { pdb, seqs, chains,
+ new String(protocol) });
}
+ }
+ }
- pdb.setFile(param);
+ pdbFileCount++;
+ } while (param != null || pdbFileCount < 10);
+ if (pdbs.size() > 0)
+ {
+ SequenceI[][] seqs = new SequenceI[pdbs.size()][];
+ PDBEntry[] pdb = new PDBEntry[pdbs.size()];
+ String[][] chains = new String[pdbs.size()][];
+ String[] protocols = new String[pdbs.size()];
+ for (int pdbsi = 0, pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)
+ {
+ Object[] o = (Object[]) pdbs.elementAt(pdbsi);
+ pdb[pdbsi] = (PDBEntry) o[0];
+ seqs[pdbsi] = (SequenceI[]) o[1];
+ chains[pdbsi] = (String[]) o[2];
+ protocols[pdbsi] = (String) o[3];
+ }
+ alignFrame.alignedStructureView(applet, pdb, seqs, chains,
+ protocols);
+ result = true;
+ }
+ return result;
+ }
- if(seqs!=null)
- {
- for (int i = 0; i < seqs.length; i++)
- {
- ( (Sequence) seqs[i]).addPDBId(pdb);
- }
+ /**
+ * 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 = setProtocolState(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();
+ }
+ }
+ return result;
+ }
- if (jmolAvailable)
- {
- new jalview.appletgui.AppletJmol(pdb,
- seqs,
- chains,
- currentAlignFrame.alignPanel,
- protocol);
- lastFrameX += 40;
- lastFrameY+=40;
- }
- else
- new MCview.AppletPDBViewer(pdb,
- seqs,
- chains,
- currentAlignFrame.alignPanel,
- protocol);
- }
- }
+ /**
+ * 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 = setProtocolState(param);
- pdbFileCount++;
+ if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
+ param, protocol))
+ {
+ alignFrame.alignPanel.fontChanged();
+ alignFrame.alignPanel.setScrollValues(0, 0);
+ result = true;
}
- while(pdbFileCount < 10);
-
- /////////////////////////////
- // modify display of features
- //
- // hide specific groups
- param = getParameter("hidefeaturegroups");
- if (param != null)
+ else
{
- applet.setFeatureGroupState(param, false);
+ System.err
+ .println("Annotations were not added from annotation file '"
+ + param + "'");
}
- // show specific groups
- param = getParameter("showfeaturegroups");
- if (param != null)
+ }
+ return result;
+ }
+
+ /**
+ * Load features file and view settings as specified by parameters. Returns
+ * true if features were loaded, else false.
+ *
+ * @param alignFrame
+ * @return
+ */
+ protected boolean loadFeatures(AlignFrame alignFrame)
+ {
+ boolean result = false;
+ // ///////////////////////////
+ // modify display of features
+ // we do this before any features have been loaded, ensuring any hidden
+ // groups are hidden when features first displayed
+ //
+ // hide specific groups
+ //
+ String param = applet.getParameter("hidefeaturegroups");
+ if (param != null)
+ {
+ alignFrame.setFeatureGroupState(separatorListToArray(param), false);
+ // applet.setFeatureGroupStateOn(newAlignFrame, param, false);
+ }
+ // show specific groups
+ param = applet.getParameter("showfeaturegroups");
+ if (param != null)
+ {
+ alignFrame.setFeatureGroupState(separatorListToArray(param), true);
+ // applet.setFeatureGroupStateOn(newAlignFrame, param, true);
+ }
+ // and now load features
+ param = applet.getParameter("features");
+ if (param != null)
+ {
+ param = setProtocolState(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 = setProtocolState(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)
{
- applet.setFeatureGroupState(param, true);
+ ex.printStackTrace();
}
}
- else
- {
- fileFound = false;
- remove(launcher);
- repaint();
- }
+ return result;
}
/**
* Discovers whether the given file is in the Applet Archive
- * @param file String
+ *
+ * @param file
+ * String
* @return boolean
*/
boolean inArchive(String file)
{
- //This might throw a security exception in certain browsers
- //Netscape Communicator for instance.
+ // This might throw a security exception in certain browsers
+ // Netscape Communicator for instance.
try
{
- return (getClass().getResourceAsStream("/" + file) != null);
- }
- catch (Exception ex)
+ boolean rtn = (getClass().getResourceAsStream("/" + file) != null);
+ if (debug)
+ {
+ System.err.println("Resource '" + file + "' was "
+ + (rtn ? "" : "not") + " located by classloader.");
+ }
+ return rtn;
+ } catch (Exception ex)
{
- System.out.println("Exception checking resources: " + file + " " + ex);
+ System.out.println("Exception checking resources: " + file + " "
+ + ex);
return false;
}
}
- String addProtocol(String file)
+ /**
+ * If the file is not already in URL format, tries to locate it by resolving
+ * as a URL.
+ *
+ * @param f
+ * @return
+ */
+ String addProtocol(final String f)
{
- if (file.indexOf("://") == -1)
+ if (f.indexOf("://") != -1)
{
- file = getCodeBase() + file;
+ // already has URL format
+ return f;
}
- return file;
+ /*
+ * Try relative to document base
+ */
+ URL documentBase = getDocumentBase();
+ String url = applet.resolveUrlForLocalOrAbsolute(f, documentBase);
+ if (urlExists(url))
+ {
+ if (debug)
+ {
+ System.err.println("Prepended document base '" + documentBase
+ + "' to make: '" + url + "'");
+ }
+ return url;
+ }
+
+ /*
+ * Try relative to codebase
+ */
+ URL codeBase = getCodeBase();
+ url = applet.resolveUrlForLocalOrAbsolute(f, codeBase);
+ if (urlExists(url))
+ {
+ if (debug)
+ {
+ System.err.println("Prepended codebase '" + codeBase
+ + "' to make: '" + url + "'");
+ }
+ return url;
+ }
+
+ return f;
+ }
+
+ /**
+ * Returns true if an input stream can be opened on the specified URL, else
+ * false.
+ *
+ * @param url
+ * @return
+ */
+ private boolean urlExists(String url)
+ {
+ InputStream is = null;
+ try
+ {
+ is = new URL(url).openStream();
+ if (is != null)
+ {
+ return true;
+ }
+ } catch (Exception x)
+ {
+ // ignore
+ } finally
+ {
+ if (is != null)
+ {
+ try
+ {
+ is.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
+ }
+ return false;
+ }
+ }
+
+ /**
+ * @return the default alignFrame acted on by the public applet methods. May
+ * return null with an error message on System.err indicating the
+ * fact.
+ */
+ public AlignFrame getDefaultTargetFrame()
+ {
+ if (currentAlignFrame != null)
+ {
+ return currentAlignFrame;
+ }
+ if (initialAlignFrame != null)
+ {
+ return initialAlignFrame;
}
+ System.err
+ .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
+ return null;
}
- public String[] tabbedListToArray(String list)
+ /**
+ * separator used for separatorList
+ */
+ protected String separator = "" + ((char) 0x00AC); // the default used to be
+ // '|' but many sequence
+ // IDS include pipes.
+
+ /**
+ * set to enable the URL based javascript execution mechanism
+ */
+ public boolean jsfallbackEnabled = false;
+
+ /**
+ * parse the string into a list
+ *
+ * @param list
+ * @return elements separated by separator
+ */
+ public String[] separatorListToArray(String list)
+ {
+ return separatorListToArray(list, separator);
+ }
+
+ /**
+ * parse the string into a list
+ *
+ * @param list
+ * @param separator
+ * @return elements separated by separator
+ */
+ public String[] separatorListToArray(String list, String separator)
{
- if (list==null || list.equals(""))
+ 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("\t",cp))>cp)
+ int cp = 0, pos;
+ while ((pos = list.indexOf(separator, cp)) > cp)
{
- jv.addElement(list.substring(cp,pos));
- cp = pos+1;
+ jv.addElement(list.substring(cp, pos));
+ cp = pos + seplen;
}
- if (cp0)
- { String[] v = new String[jv.size()];
- jv.copyInto(v);
+ if (jv.size() > 0)
+ {
+ String[] v = new String[jv.size()];
+ for (int i = 0; i < v.length; i++)
+ {
+ v[i] = (String) jv.elementAt(i);
+ }
jv.removeAllElements();
if (debug)
{
- System.err.println("Array from Tabbed List:\n"+v.length+"\n"+v.toString());
+ System.err.println("Array from '" + separator
+ + "' separated List:\n" + v.length);
+ for (int i = 0; i < v.length; i++)
+ {
+ System.err.println("item " + i + " '" + v[i] + "'");
+ }
}
return v;
}
if (debug)
{
- System.err.println("Empty Array from Tabbed List");
+ System.err.println("Empty Array from '" + separator
+ + "' separated List");
}
return null;
}
- public String ArraytotabbedList(String[] list)
+ /**
+ * concatenate the list with separator
+ *
+ * @param list
+ * @return concatenated string
+ */
+ public String arrayToSeparatorList(String[] list)
+ {
+ return arrayToSeparatorList(list, separator);
+ }
+
+ /**
+ * concatenate the list with separator
+ *
+ * @param list
+ * @param separator
+ * @return concatenated string
+ */
+ public String arrayToSeparatorList(String[] list, String separator)
{
StringBuffer v = new StringBuffer();
- if (list!=null)
+ if (list != null && list.length > 0)
{
- for (int i=0,iSize=list.length-1;i 0)
+ {
+ v.append(separator);
+ }
+ v.append(list[i]);
}
- v.append("\t");
- }
- if (list[list.length-1]!=null)
- { v.append(list[list.length-1]);
}
if (debug)
{
- System.err.println("Tabbed List:\n"+v.toString());
+ System.err.println("Returning '" + separator
+ + "' separated List:\n");
+ System.err.println(v);
}
return v.toString();
}
if (debug)
{
- System.err.println("Empty Tabbed List\n");
+ System.err.println("Returning empty '" + separator
+ + "' separated List\n");
}
- return "";
+ return "" + separator;
}
- /**
- * @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroups()
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
*/
public String getFeatureGroups()
{
- String lst = ArraytotabbedList(currentAlignFrame.getFeatureGroups());
+ String lst = arrayToSeparatorList(getDefaultTargetFrame()
+ .getFeatureGroups());
+ return lst;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame
+ * )
+ */
+ public String getFeatureGroupsOn(AlignFrame alf)
+ {
+ String lst = arrayToSeparatorList(alf.getFeatureGroups());
return lst;
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)
+ */
+ public String getFeatureGroupsOfState(boolean visible)
+ {
+ return arrayToSeparatorList(getDefaultTargetFrame()
+ .getFeatureGroupsOfState(visible));
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui
+ * .AlignFrame, boolean)
+ */
+ public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
+ {
+ return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui.
+ * AlignFrame, java.lang.String, boolean)
+ */
+ public void setFeatureGroupStateOn(final AlignFrame alf,
+ final String groups, boolean state)
+ {
+ final boolean st = state;// !(state==null || state.equals("") ||
+ // state.toLowerCase().equals("false"));
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ 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);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getSeparator()
+ */
+ public String getSeparator()
+ {
+ return separator;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @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 + "'");
+ }
+ }
+
+ /**
+ * get boolean value of applet parameter 'name' and return default if
+ * parameter is not set
+ *
+ * @param name
+ * name of paremeter
+ * @param def
+ * the value to return otherwise
+ * @return true or false
+ */
+ public boolean getDefaultParameter(String name, boolean def)
+ {
+ String stn;
+ if ((stn = getParameter(name)) == null)
+ {
+ return def;
+ }
+ if (TRUE.equalsIgnoreCase(stn))
+ {
+ return true;
+ }
+ return false;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame,
+ * java.lang.String, java.lang.String, java.lang.String)
+ */
+ public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
+ String pdbEntryString, String pdbFile)
+ {
+ return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);
+ }
+
+ protected void setAlignPdbStructures(boolean alignPdbStructures)
+ {
+ this.alignPdbStructures = alignPdbStructures;
+ }
+
+ public boolean isAlignPdbStructures()
+ {
+ return alignPdbStructures;
+ }
+
+ 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;
+ }
+
/**
- * @param visible
+ * return the given colour value parameter or the given default if parameter
+ * not given
+ *
+ * @param colparam
+ * @param defcolour
* @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
*/
- public String getFeatureGroupsOfState(boolean visible)
+ public Color getDefaultColourParameter(String colparam, Color defcolour)
+ {
+ String colprop = getParameter(colparam);
+ if (colprop == null || colprop.trim().length() == 0)
+ {
+ return defcolour;
+ }
+ Color col = jalview.schemes.ColourSchemeProperty
+ .getAWTColorFromName(colprop);
+ if (col == null)
+ {
+ try
+ {
+ 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()
{
- return ArraytotabbedList(currentAlignFrame.getFeatureGroupsOfState(visible));
+ String helpUrl = getParameter("jalviewhelpurl");
+ if (helpUrl == null || helpUrl.trim().length() < 5)
+ {
+ helpUrl = "http://www.jalview.org/help.html";
+ }
+ showURL(helpUrl, "HELP");
}
+
/**
- * @param groups tab separated list of group names
- * @param state true or false
- * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[], boolean)
+ * 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
*/
- public void setFeatureGroupState(AlignFrame alf, String groups, boolean state)
+ private String resolveUrlForLocalOrAbsolute(String url, URL localref)
{
- boolean st = state;//!(state==null || state.equals("") || state.toLowerCase().equals("false"));
- alf.setFeatureGroupState(tabbedListToArray(groups), st);
+ String codebase = localref.toString();
+ if (url.indexOf("/") == 0)
+ {
+ String localfile = localref.getFile();
+ url = codebase.substring(0, codebase.length() - localfile.length())
+ + url;
+ }
+ else
+ {
+ url = localref + url;
+ }
+ if (debug)
+ {
+ System.err.println("URL: " + localref.toString());
+ System.err.println("URL.getFile: " + localref.getFile());
+ System.err.println("URL.getPath: " + localref.getPath());
+ System.err.println("URL.getQuery: " + localref.getQuery());
+ System.err.println("returning " + url);
+ }
+ return url;
}
- public void setFeatureGroupState(String groups, boolean state)
+
+ /**
+ * 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)
{
- setFeatureGroupState(currentAlignFrame, groups, state);
+ 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)
+ {
+ System.err
+ .println("Show url (prepended "
+ + prepend
+ + " - toggle resolvetocodebase if code/docbase resolution is wrong): "
+ + url);
+ }
+ }
+ else
+ {
+ if (debug)
+ {
+ System.err.println("Show url: " + url);
+ }
+ }
+ if (url.indexOf("javascript:") == 0)
+ {
+ // no target for the javascript context
+ getAppletContext().showDocument(new java.net.URL(url));
+ }
+ else
+ {
+ getAppletContext().showDocument(new java.net.URL(url), target);
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
}
+
+ /**
+ * bind structures in a viewer to any matching sequences in an alignFrame (use
+ * sequenceIds to limit scope of search to specific sequences)
+ *
+ * @param alFrame
+ * @param viewer
+ * @param sequenceIds
+ * @return TODO: consider making an exception structure for indicating when
+ * binding fails public SequenceStructureBinding
+ * addStructureViewInstance( AlignFrame alFrame, Object viewer, String
+ * sequenceIds) {
+ *
+ * if (sequenceIds != null && sequenceIds.length() > 0) { return
+ * alFrame.addStructureViewInstance(viewer,
+ * separatorListToArray(sequenceIds)); } else { return
+ * alFrame.addStructureViewInstance(viewer, null); } // return null; }
+ */
}