X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=33ff254843809cd69fed6e15972bc8b296394612;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=0623193b5b1ccaea808d166fe067c4de80e9e28a;hpb=d982e0264da4cd35cb993144754e797db11c8c48;p=jalview.git diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java old mode 100755 new mode 100644 index 0623193..33ff254 --- a/src/jalview/bin/JalviewLite.java +++ b/src/jalview/bin/JalviewLite.java @@ -1,573 +1,2113 @@ /* - * 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 - * 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. - * - * 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.bin; -import java.applet.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.appletgui.*; -import jalview.datamodel.*; -import jalview.io.*; +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; +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.JnetAnnotationMaker; +import jalview.javascript.JSFunctionExec; +import jalview.javascript.JalviewLiteJsApi; +import jalview.javascript.JsCallBack; +import jalview.structure.SelectionListener; +import jalview.structure.StructureSelectionManager; + +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.InputStreamReader; +import java.net.URL; +import java.util.Hashtable; +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 { + 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 getSelectedSequencesFrom(getDefaultTargetFrame()); + } - /////////////////////////////////////////// - //The following public methods maybe called - //externally, eg via javascript in HTML page + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String) + */ + public String getSelectedSequences(String sep) + { + return getSelectedSequencesFrom(getDefaultTargetFrame(), sep); + } - public String getSelectedSequences() + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui + * .AlignFrame) + */ + public String getSelectedSequencesFrom(AlignFrame alf) { - StringBuffer result = new StringBuffer(""); + return getSelectedSequencesFrom(alf, separator); // ""+0x00AC); + } - if (initialAlignFrame.viewport.getSelectionGroup() != null) + /* + * (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 = initialAlignFrame.viewport.getSelectionGroup(). - getSequencesInOrder( - initialAlignFrame.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(format, "true"); + highlightIn(getDefaultTargetFrame(), sequenceId, position, + alignedPosition); } - public String getAlignment(String format, String suffix) + /* + * (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) { - try - { - boolean seqlimits = suffix.equalsIgnoreCase("true"); - - String reply = new AppletFormatAdapter().formatSequences(format, - currentAlignFrame.viewport.getAlignment(), seqlimits); - return reply; - } - catch (Exception ex) + // 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) { - ex.printStackTrace(); - return "Error retrieving alignment in " + format + " format. "; + 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 void loadAnnotation(String annotation) + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String, + * java.lang.String) + */ + public void select(String sequenceIds, String columns) { - if (new AnnotationFile().readAnnotationFile( - currentAlignFrame.getAlignViewport().getAlignment(), annotation, - AppletFormatAdapter.PASTE)) - { - currentAlignFrame.alignPanel.fontChanged(); - currentAlignFrame.alignPanel.setScrollValues(0, 0); - } - else - { - currentAlignFrame.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE); - } + selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator); } - public String getFeatures(String 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) { - return currentAlignFrame.outputFeatures(false, format); + selectIn(getDefaultTargetFrame(), sequenceIds, columns, sep); } - public String getAnnotation() + /* + * (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) { - return currentAlignFrame.outputAnnotations(false); + selectIn(alf, sequenceIds, columns, separator); } - public void loadAlignment(String text, String title) + /* + * (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) { - Alignment al = null; - String format = new IdentifyFile().Identify(text, AppletFormatAdapter.PASTE); - try + if (sep == null || sep.length() == 0) { - al = new AppletFormatAdapter().readFile(text, - AppletFormatAdapter.PASTE, - format); - if (al.getHeight() > 0) + sep = separator; + } + else + { + if (debug) { - new AlignFrame(al, this, title, false); + System.err.println("Selecting region using separator string '" + + separator + "'"); } } - catch (java.io.IOException ex) + // 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) { - ex.printStackTrace(); + 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) + { + 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); + } + }); } } - //////////////////////////////////////////////// - //////////////////////////////////////////////// - - - - static int lastFrameX = 200; - static int lastFrameY = 200; - boolean fileFound = true; - String file = "No file"; - Button launcher = new Button("Start Jalview"); - - //The currentAlignFrame is static, it will change - //if and when the user selects a new window - public static AlignFrame currentAlignFrame; - - //This is the first frame to be displayed, and does not change - AlignFrame initialAlignFrame; - - boolean embedded = false; - - public boolean jmolAvailable = false; + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignment(java.lang. + * String, java.lang.String) + */ + public String getSelectedSequencesAsAlignment(String format, String suffix) + { + return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(), + format, suffix); + } - /** - * init method for Jalview Applet + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignmentFrom(jalview + * .appletgui.AlignFrame, java.lang.String, java.lang.String) */ - public void init() + public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, + String format, String suffix) { try { - Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter", - true, Thread.currentThread().getContextClassLoader()); - - jmolAvailable = true; - } - catch (java.lang.ClassNotFoundException ex) + boolean seqlimits = suffix.equalsIgnoreCase("true"); + if (alf.viewport.getSelectionGroup() != null) + { + String reply = new AppletFormatAdapter().formatSequences(format, + new Alignment(alf.viewport.getSelectionAsNewSequence()), + seqlimits); + return reply; + } + } catch (Exception ex) { - System.out.println("Jmol not found - Use MCview for structures"); + ex.printStackTrace(); + return "Error retrieving alignment in " + format + " format. "; } + return ""; + } - int r = 255; - int g = 255; - int b = 255; - String param = getParameter("RGB"); + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder() + */ + public String getAlignmentOrder() + { + return getAlignmentOrderFrom(getDefaultTargetFrame()); + } - if (param != null) - { - try - { - r = Integer.parseInt(param.substring(0, 2), 16); - g = Integer.parseInt(param.substring(2, 4), 16); - b = Integer.parseInt(param.substring(4, 6), 16); - } - catch (Exception ex) - { - r = 255; - g = 255; - b = 255; - } - } + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame + * ) + */ + public String getAlignmentOrderFrom(AlignFrame alf) + { + return getAlignmentOrderFrom(alf, separator); + } - param = getParameter("label"); - if (param != null) + /* + * (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++) { - launcher.setLabel(param); + order[i] = alorder.getSequenceAt(i).getName(); } + return arrayToSeparatorList(order); + } - this.setBackground(new Color(r, g, b)); + /* + * (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); + } - file = getParameter("file"); + /* + * (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); + } - if (file == null) + /* + * (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) { - //Maybe the sequences are added as parameters - StringBuffer data = new StringBuffer("PASTE"); - int i = 1; - while ( (file = getParameter("sequence" + i)) != null) + 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++) { - data.append(file.toString() + "\n"); - i++; + if (ids[i].trim().length() == 0) + { + continue; + } + SequenceI sq = matcher.findIdMatch(ids[i]); + if (sq != null) + { + sqs[s++] = sq; + } } - if (data.length() > 5) + if (s > 0) { - file = data.toString(); + SequenceI[] sqq = new SequenceI[s]; + System.arraycopy(sqs, 0, sqq, 0, s); + sqs = sqq; + } + else + { + sqs = null; } } - - final JalviewLite applet = this; - if (getParameter("embedded") != null - && getParameter("embedded").equalsIgnoreCase("true")) + if (sqs == null) { - embedded = true; - LoadingThread loader = new LoadingThread(file, applet); - loader.start(); + return ""; } - else if (file != null) - { - add(launcher); + ; + final AlignmentOrder aorder = new AlignmentOrder(sqs); - launcher.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - LoadingThread loader = new LoadingThread(file, - applet); - loader.start(); - } - }); - } - else + if (undoName != null && undoName.trim().length() == 0) { - file = "NO FILE"; - fileFound = false; + 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" : ""; } - public static void main(String[] args) + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String) + */ + public String getAlignment(String format) { - if (args.length != 1) - { - System.out.println("\nUsage: java -jar jalviewApplet.jar fileName\n"); - System.exit(1); - } + 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"); + } - String format = new jalview.io.IdentifyFile().Identify(args[0], - AppletFormatAdapter.FILE); + /* + * (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); + } - Alignment al = null; + /* + * (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) + { try { - al = new AppletFormatAdapter().readFile(args[0], AppletFormatAdapter.FILE, - format); - } - catch (java.io.IOException ex) + boolean seqlimits = suffix.equalsIgnoreCase("true"); + + String reply = new AppletFormatAdapter().formatSequences(format, + alf.viewport.getAlignment(), seqlimits); + return reply; + } catch (Exception ex) { ex.printStackTrace(); - } - if ( (al != null) && (al.getHeight() > 0)) - { - AlignFrame af = new AlignFrame(al, null, args[0], false); - af.statusBar.setText("Successfully loaded file " + args[0]); + return "Error retrieving alignment in " + format + " format. "; } } - /** - * 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 + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String) */ - public static void addFrame(final Frame frame, String title, int width, - int height) + public void loadAnnotation(String annotation) { - frame.setLocation(lastFrameX, lastFrameY); - lastFrameX += 40; - lastFrameY += 40; - frame.setSize(width, height); - frame.setTitle(title); - frame.addWindowListener(new WindowAdapter() - { - public void windowClosing(WindowEvent e) - { - if (frame instanceof AlignFrame) - { - ( (AlignFrame) frame).closeMenuItem_actionPerformed(); - } - if (currentAlignFrame == frame) - { - currentAlignFrame = null; - } - lastFrameX -= 40; - lastFrameY -= 40; - frame.setMenuBar(null); - frame.dispose(); - } - - public void windowActivated(WindowEvent e) - { - if (frame instanceof AlignFrame) - { - currentAlignFrame = (AlignFrame) frame; - } - } - - }); - frame.setVisible(true); + loadAnnotationFrom(getDefaultTargetFrame(), annotation); } - /** - * This paints the background surrounding the "Launch Jalview button" - *
- *
If file given in parameter not found, displays error message - * - * @param g graphics context + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame + * , java.lang.String) */ - public void paint(Graphics g) + public void loadAnnotationFrom(AlignFrame alf, String annotation) { - if (!fileFound) + if (new AnnotationFile().readAnnotationFile(alf.getAlignViewport() + .getAlignment(), annotation, AppletFormatAdapter.PASTE)) { - g.setColor(new Color(200, 200, 200)); - g.setColor(Color.cyan); - g.fillRect(0, 0, getSize().width, getSize().height); - g.setColor(Color.red); - g.drawString("Jalview can't open file", 5, 15); - g.drawString("\"" + file + "\"", 5, 30); + alf.alignPanel.fontChanged(); + alf.alignPanel.setScrollValues(0, 0); } - else if (embedded) + else { - 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); + alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE); } + } + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String) + */ + public String getFeatures(String format) + { + return getFeaturesFrom(getDefaultTargetFrame(), format); } - class LoadingThread - extends Thread + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame, + * java.lang.String) + */ + public String getFeaturesFrom(AlignFrame alf, String format) { - String file; - String protocol; - String format; - JalviewLite applet; + 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) + { + Alignment al = null; - public LoadingThread(String _file, - JalviewLite _applet) + String format = new IdentifyFile().Identify(text, + AppletFormatAdapter.PASTE); + try { - file = _file; - if (file.startsWith("PASTE")) + al = new AppletFormatAdapter().readFile(text, + AppletFormatAdapter.PASTE, format); + if (al.getHeight() > 0) { - file = file.substring(5); - protocol = AppletFormatAdapter.PASTE; + return new AlignFrame(al, this, title, false); } - else if (inArchive(file)) + } 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) { - protocol = AppletFormatAdapter.CLASSLOADER; + System.err + .println("jalview Javascript error: Ignoring empty function for mouseover listener."); + return; } - else + } + 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) { - file = addProtocol(file); - protocol = AppletFormatAdapter.URL; + System.err + .println("jalview Javascript error: Ignoring empty function for selection listener."); + return; } - format = new jalview.io.IdentifyFile().Identify(file, protocol); - applet = _applet; } + 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."); + } + } - public void run() + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String, + * java.lang.String) + */ + public void setStructureListener(String listener, String modelSet) + { + if (listener != null) { - Alignment al = null; - try + listener = listener.trim(); + if (listener.length() == 0) { - al = new AppletFormatAdapter().readFile(file, protocol, - format); + System.err + .println("jalview Javascript error: Ignoring empty function for selection listener."); + return; } - catch (java.io.IOException ex) + } + 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) { - ex.printStackTrace(); + listener = null; } - if ( (al != null) && (al.getHeight() > 0)) + } + 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))) { - currentAlignFrame = new AlignFrame(al, - applet, - file, - embedded); - - if (protocol == jalview.io.AppletFormatAdapter.PASTE) + 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) { - currentAlignFrame.setTitle("Sequences from " + getDocumentBase()); + System.err.println("Removed listener '" + listener + "'"); } + } + else + { + ms++; + } + } + if (rprt) + { + System.err.println("There are now " + javascriptListeners.size() + + " listeners in total."); + } + } - initialAlignFrame = currentAlignFrame; + public void stop() + { + System.err.println("Applet " + getName() + " stop()."); + tidyUp(); + } - currentAlignFrame.statusBar.setText("Successfully loaded file " + file); + public void destroy() + { + System.err.println("Applet " + getName() + " destroy()."); + tidyUp(); + } - String treeFile = applet.getParameter("tree"); - if (treeFile == null) + 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) { - treeFile = applet.getParameter("treeFile"); + StructureSelectionManager.getStructureSelectionManager(this) + .removeSelectionListener((SelectionListener) mol); } - - if (treeFile != null) + else { - try - { - if (inArchive(treeFile)) - { - protocol = AppletFormatAdapter.CLASSLOADER; - } - else - { - protocol = AppletFormatAdapter.URL; - treeFile = addProtocol(treeFile); - } - - jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile, - protocol); + 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); + } - fin.parse(); + private jalview.javascript.JSFunctionExec jsFunctionExec; - if (fin.getTree() != null) - { - currentAlignFrame.loadTree(fin, treeFile); - } - } - catch (Exception ex) + /* + * (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) { - ex.printStackTrace(); + System.err.println("mouseOver for '" + pdbResNum + + "' in chain '" + chain + "' in structure '" + pdbfile + + "'"); } + } catch (NumberFormatException e) + { + System.err.println("Ignoring invalid residue number string '" + + pdbResNum + "'"); } - String param = getParameter("features"); - if (param != null) - { - if (!inArchive(param)) - { - param = addProtocol(param); - } + } + }); + } - currentAlignFrame.parseFeaturesFile(param, protocol); - } + /* + * (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()); - param = getParameter("showFeatureSettings"); - if (param != null && param.equalsIgnoreCase("true")) + } catch (Exception ex) { - currentAlignFrame.viewport.showSequenceFeatures(true); - new FeatureSettings(currentAlignFrame.alignPanel); + System.err.println("Couldn't parse integer arguments (topRow='" + + topRow + "' and leftHandColumn='" + leftHandColumn + + "')"); + ex.printStackTrace(); } + } + }); + } - param = getParameter("annotations"); - if (param != null) + /* + * (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 { - if (!inArchive(param)) - { - param = addProtocol(param); - } + alf.scrollToRow(new Integer(topRow).intValue()); - new AnnotationFile().readAnnotationFile( - currentAlignFrame.viewport.getAlignment(), - param, - protocol); + } catch (Exception ex) + { + System.err.println("Couldn't parse integer arguments (topRow='" + + topRow + "')"); + ex.printStackTrace(); + } - currentAlignFrame.alignPanel.fontChanged(); - currentAlignFrame.alignPanel.setScrollValues(0, 0); + } + }); + } - } + /* + * (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() + { - param = getParameter("jnetfile"); - if (param != null) + @Override + public void run() + { + try { - try - { - if (inArchive(param)) - { - protocol = AppletFormatAdapter.CLASSLOADER; - } - else - { - protocol = AppletFormatAdapter.URL; - param = addProtocol(param); - } + alf.scrollToColumn(new Integer(leftHandColumn).intValue()); - 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) - { - ex.printStackTrace(); - } + } catch (Exception ex) + { + System.err + .println("Couldn't parse integer arguments (leftHandColumn='" + + leftHandColumn + "')"); + ex.printStackTrace(); } + } + }); + } - param = getParameter("PDBFILE"); - if (param != null) - { + // ////////////////////////////////////////////// + // ////////////////////////////////////////////// - PDBEntry pdb = new PDBEntry(); + public static int lastFrameX = 200; - if (!inArchive(param) || jmolAvailable) - { - param = addProtocol(param); - } + public static int lastFrameY = 200; - pdb.setFile(param); + boolean fileFound = true; - String sequence = applet.getParameter("PDBSEQ"); + String file = "No file"; - if (sequence != null) + Button launcher = new Button("Start Jalview"); + + /** + * The currentAlignFrame is static, it will change if and when the user + * selects a new window. Note that it will *never* point back to the embedded + * AlignFrame if the applet is started as embedded on the page and then + * afterwards a new view is created. + */ + 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; + + private static void initBuildDetails() + { + if (builddate == null) + { + builddate = "unknown"; + version = "test"; + 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); + } + } + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + } + } + + public static String getBuildDate() + { + initBuildDetails(); + return builddate; + } + + 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 + */ + String dbg = getParameter("debug"); + if (dbg != null) + { + debug = dbg.toLowerCase().equals("true"); + } + if (debug) + { + + System.err.println("JalviewLite Version " + getVersion()); + System.err.println("Build Date : " + getBuildDate()); + + } + 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( + "Invalid separator parameter - must be non-zero length"); + } + } + int r = 255; + int g = 255; + int b = 255; + String param = getParameter("RGB"); + + if (param != null) + { + try + { + r = Integer.parseInt(param.substring(0, 2), 16); + g = Integer.parseInt(param.substring(2, 4), 16); + b = Integer.parseInt(param.substring(4, 6), 16); + } catch (Exception ex) + { + r = 255; + g = 255; + b = 255; + } + } + param = getParameter("label"); + if (param != null) + { + launcher.setLabel(param); + } + + setBackground(new Color(r, g, b)); + + file = getParameter("file"); + + if (file == null) + { + // Maybe the sequences are added as parameters + StringBuffer data = new StringBuffer("PASTE"); + int i = 1; + while ((file = getParameter("sequence" + i)) != null) + { + data.append(file.toString() + "\n"); + i++; + } + if (data.length() > 5) + { + file = data.toString(); + } + } + + 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, jvapplet); + loader.start(); + } + else if (file != null) + { + if (getParameter("showbutton") == null + || !getParameter("showbutton").equalsIgnoreCase("false")) + { + // Add the JalviewLite 'Button' to the page + add(launcher); + launcher.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + LoadingThread loader = new LoadingThread(file, 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 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) + { + } + ; + if (scriptObject != null) + { + try + { + // do onInit with the JS executor thread + new JSFunctionExec(this).executeJavascriptFunction(true, + initjscallback, null, "Calling oninit callback '" + + initjscallback + "'."); + } catch (Exception e) + { + System.err.println("Exception when executing _oninit callback '" + + initjscallback + "'."); + e.printStackTrace(); + } + } + else + { + System.err.println("Not executing _oninit callback '" + + initjscallback + "' - no scripting allowed."); + } + } + } + + /** + * Initialises and displays a new java.awt.Frame + * + * @param frame + * java.awt.Frame to be displayed + * @param title + * title of new frame + * @param width + * width if new frame + * @param height + * height of new frame + */ + public static void addFrame(final Frame frame, String title, int width, + int height) + { + frame.setLocation(lastFrameX, lastFrameY); + lastFrameX += 40; + lastFrameY += 40; + frame.setSize(width, height); + frame.setTitle(title); + frame.addWindowListener(new WindowAdapter() + { + public void windowClosing(WindowEvent e) + { + if (frame instanceof AlignFrame) + { + AlignViewport vp = ((AlignFrame) frame).viewport; + ((AlignFrame) frame).closeMenuItem_actionPerformed(); + if (vp.applet.currentAlignFrame == frame) + { + vp.applet.currentAlignFrame = null; + } + vp.applet = null; + vp = null; + + } + lastFrameX -= 40; + lastFrameY -= 40; + if (frame instanceof EmbmenuFrame) + { + ((EmbmenuFrame) frame).destroyMenus(); + } + frame.setMenuBar(null); + frame.dispose(); + } + + public void windowActivated(WindowEvent e) + { + if (frame instanceof AlignFrame) + { + ((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame; + if (debug) + { + System.err.println("Activated window " + frame); + } + } + // be good. + super.windowActivated(e); + } + /* + * Probably not necessary to do this - see TODO above. (non-Javadoc) + * + * @see + * java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent + * ) + * + * public void windowDeactivated(WindowEvent e) { if (currentAlignFrame == + * frame) { currentAlignFrame = null; if (debug) { + * System.err.println("Deactivated window "+frame); } } + * super.windowDeactivated(e); } + */ + }); + frame.setVisible(true); + } + + /** + * This paints the background surrounding the "Launch Jalview button"
+ *
+ * If file given in parameter not found, displays error message + * + * @param g + * graphics context + */ + public void paint(Graphics g) + { + if (!fileFound) + { + g.setColor(new Color(200, 200, 200)); + g.setColor(Color.cyan); + g.fillRect(0, 0, getSize().width, getSize().height); + g.setColor(Color.red); + g.drawString("Jalview can't 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, getSize().height / 2 - 30); + g.drawString("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() + { + if (running || checkedForJmol) + { + return; + } + running = true; + if (checkForJmol) + { + try + { + if (!System.getProperty("java.version").startsWith("1.1")) + { + Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter"); + jmolAvailable = true; + } + if (!jmolAvailable) { - if (jmolAvailable) - new jalview.appletgui.AppletJmol(pdb, - new SequenceI[] - { (Sequence) currentAlignFrame. - getAlignViewport().getAlignment(). - findName(sequence)}, - currentAlignFrame.alignPanel, - protocol); + System.out + .println("Jmol not available - Using MCview for structures"); + } + } catch (java.lang.ClassNotFoundException ex) + { + } + } + else + { + 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 + { + /** + * State variable: File source + */ + String file; + + /** + * State variable: protocol for access to file source + */ + String protocol; + + /** + * State variable: format of file source + */ + String format; + + String _file; + + JalviewLite applet; + + private void dbgMsg(String msg) + { + if (applet.debug) + { + System.err.println(msg); + } + } + + /** + * 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); + protocol = AppletFormatAdapter.PASTE; + } + else if (inArchive(file)) + { + protocol = AppletFormatAdapter.CLASSLOADER; + } + else + { + file = addProtocol(file); + protocol = AppletFormatAdapter.URL; + } + dbgMsg("Protocol identified as '" + protocol + "'"); + return file; + } + + public LoadingThread(String _file, JalviewLite _applet) + { + this._file = _file; + 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(); + } + + private void startLoading() + { + AlignFrame newAlignFrame; + dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile"); + file = setProtocolState(_file); + + format = new jalview.io.IdentifyFile().Identify(file, protocol); + dbgMsg("File identified as '" + format + "'"); + dbgMsg("Loading started."); + Alignment al = null; + try + { + al = new AppletFormatAdapter().readFile(file, protocol, format); + } catch (java.io.IOException ex) + { + dbgMsg("File load exception."); + ex.printStackTrace(); + if (debug) + { + try + { + FileParse fp = new FileParse(file, protocol); + String ln = null; + dbgMsg(">>>Dumping contents of '" + file + "' " + "(" + + protocol + ")"); + while ((ln = fp.nextLine()) != null) + { + dbgMsg(ln); + } + dbgMsg(">>>Dump finished."); + } catch (Exception e) + { + System.err + .println("Exception when trying to dump the content of the file parameter."); + e.printStackTrace(); + } + } + } + if ((al != null) && (al.getHeight() > 0)) + { + dbgMsg("Successfully loaded file."); + newAlignFrame = new AlignFrame(al, applet, file, embedded); + if (initialAlignFrame == null) + { + initialAlignFrame = newAlignFrame; + } + // update the focus. + currentAlignFrame = newAlignFrame; + + if (protocol == jalview.io.AppletFormatAdapter.PASTE) + { + newAlignFrame.setTitle("Sequences from " + + applet.getDocumentBase()); + } + + newAlignFrame.statusBar.setText("Successfully loaded file " + file); + + String treeFile = applet.getParameter("tree"); + if (treeFile == null) + { + treeFile = applet.getParameter("treeFile"); + } + + if (treeFile != null) + { + try + { + treeFile = setProtocolState(treeFile); + /* + * if (inArchive(treeFile)) { protocol = + * AppletFormatAdapter.CLASSLOADER; } else { protocol = + * AppletFormatAdapter.URL; treeFile = addProtocol(treeFile); } + */ + jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile, + protocol); + + fin.parse(); + + if (fin.getTree() != null) + { + newAlignFrame.loadTree(fin, treeFile); + dbgMsg("Successfuly imported tree."); + } + else + { + dbgMsg("Tree parameter did not resolve to a valid tree."); + } + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + + String param = applet.getParameter("features"); + if (param != null) + { + param = setProtocolState(param); + + newAlignFrame.parseFeaturesFile(param, protocol); + } + + param = applet.getParameter("showFeatureSettings"); + if (param != null && param.equalsIgnoreCase("true")) + { + newAlignFrame.viewport.showSequenceFeatures(true); + new FeatureSettings(newAlignFrame.alignPanel); + } + + param = applet.getParameter("annotations"); + if (param != null) + { + param = setProtocolState(param); + + if (new AnnotationFile().readAnnotationFile( + newAlignFrame.viewport.getAlignment(), param, protocol)) + { + newAlignFrame.alignPanel.fontChanged(); + newAlignFrame.alignPanel.setScrollValues(0, 0); + } + else + { + System.err + .println("Annotations were not added from annotation file '" + + param + "'"); + } + + } + + param = applet.getParameter("jnetfile"); + if (param != null) + { + try + { + param = setProtocolState(param); + jalview.io.JPredFile predictions = new jalview.io.JPredFile( + param, protocol); + JnetAnnotationMaker.add_annotation(predictions, + newAlignFrame.viewport.getAlignment(), 0, false); // false==do + // not + // add + // sequence + // profile + // from + // concise + // output + newAlignFrame.alignPanel.fontChanged(); + newAlignFrame.alignPanel.setScrollValues(0, 0); + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + /* + * 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( + newAlignFrame.getAlignViewport().getAlignment() + .getSequencesArray()) : null; + + do + { + if (pdbFileCount > 0) + { + param = applet.getParameter("PDBFILE" + pdbFileCount); + } + else + { + param = applet.getParameter("PDBFILE"); + } + + if (param != null) + { + PDBEntry pdb = new PDBEntry(); + + String seqstring; + SequenceI[] seqs = null; + String[] chains = null; + + StringTokenizer st = new StringTokenizer(param, " "); + + if (st.countTokens() < 2) + { + String sequence = applet.getParameter("PDBSEQ"); + if (sequence != null) + seqs = new SequenceI[] + { matcher == null ? (Sequence) newAlignFrame + .getAlignViewport().getAlignment() + .findName(sequence) : matcher.findIdMatch(sequence) }; + + } else + { + param = st.nextToken(); + Vector tmp = new Vector(); + Vector tmp2 = new Vector(); + + while (st.hasMoreTokens()) + { + seqstring = st.nextToken(); + StringTokenizer st2 = new StringTokenizer(seqstring, "="); + if (st2.countTokens() > 1) + { + // This is the chain + tmp2.addElement(st2.nextToken()); + seqstring = st2.nextToken(); + } + tmp.addElement(matcher == null ? (Sequence) newAlignFrame + .getAlignViewport().getAlignment() + .findName(seqstring) : matcher + .findIdMatch(seqstring)); + } + + seqs = new SequenceI[tmp.size()]; + tmp.copyInto(seqs); + if (tmp2.size() == tmp.size()) + { + chains = new String[tmp2.size()]; + tmp2.copyInto(chains); + } + } + param = setProtocolState(param); + + if (// !jmolAvailable + // && + protocol == AppletFormatAdapter.CLASSLOADER + && !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 + // the local pdb file was identified in the class loader + protocol = AppletFormatAdapter.URL; // this is probably NOT + // CORRECT! + param = addProtocol(param); // + } + + pdb.setFile(param); - new MCview.AppletPDBViewer(pdb, - new SequenceI[] - { (Sequence) currentAlignFrame. - getAlignViewport().getAlignment(). - findName(sequence)}, - currentAlignFrame.alignPanel, - protocol); + if (seqs != null) + { + for (int i = 0; i < seqs.length; i++) + { + if (seqs[i] != null) + { + ((Sequence) seqs[i]).addPDBId(pdb); + } + else + { + if (JalviewLite.debug) + { + // this may not really be a problem but we give a warning + // anyway + System.err + .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence " + + i + ")"); + } + } + } + + if (!alignPdbStructures) + { + newAlignFrame.newStructureView(applet, pdb, seqs, chains, + protocol); + } + else + { + pdbs.addElement(new Object[] + { pdb, seqs, chains, new String(protocol) }); + } + } + } + + 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]; } + newAlignFrame.alignedStructureView(applet, pdb, seqs, chains, + protocols); } + // /////////////////////////// + // modify display of features + // + // hide specific groups + param = applet.getParameter("hidefeaturegroups"); + if (param != null) + { + applet.setFeatureGroupStateOn(newAlignFrame, param, false); + } + // show specific groups + param = applet.getParameter("showfeaturegroups"); + if (param != null) + { + applet.setFeatureGroupStateOn(newAlignFrame, param, true); + } } else { fileFound = false; - remove(launcher); - repaint(); + applet.remove(launcher); + applet.repaint(); } + callInitCallback(); } /** * 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; } } @@ -576,10 +2116,571 @@ public class JalviewLite { if (file.indexOf("://") == -1) { - file = getCodeBase() + file; + 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) + { + } + ; + } return file; } } + + /** + * @return the default alignFrame acted on by the public applet methods. May + * return null with an error message on System.err indicating the + * fact. + */ + public AlignFrame getDefaultTargetFrame() + { + if (currentAlignFrame != null) + { + return currentAlignFrame; + } + if (initialAlignFrame != null) + { + return initialAlignFrame; + } + System.err + .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use."); + return null; + } + + /** + * separator used for separatorList + */ + protected String separator = "" + ((char) 0x00AC); // the default used to be + // '|' but many sequence + // IDS include pipes. + + /** + * set to enable the URL based javascript execution mechanism + */ + 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) + { + // 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) + { + jv.addElement(list.substring(cp, pos)); + cp = pos + seplen; + } + if (cp < list.length()) + { + String c = list.substring(cp); + if (!c.equals(separator)) + { + jv.addElement(c); + } + } + if (jv.size() > 0) + { + String[] v = new String[jv.size()]; + for (int i = 0; i < v.length; i++) + { + v[i] = (String) jv.elementAt(i); + } + jv.removeAllElements(); + if (debug) + { + System.err.println("Array from '" + separator + + "' separated List:\n" + v.length); + for (int i = 0; i < v.length; i++) + { + System.err.println("item " + i + " '" + v[i] + "'"); + } + } + return v; + } + if (debug) + { + System.err.println("Empty Array from '" + separator + + "' separated List"); + } + return null; + } + + /** + * 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 && list.length > 0) + { + for (int i = 0, iSize = list.length; i < iSize; i++) + { + if (list[i] != null) + { + if (i > 0) + { + v.append(separator); + } + v.append(list[i]); + } + } + if (debug) + { + System.err.println("Returning '" + separator + + "' separated List:\n"); + System.err.println(v); + } + return v.toString(); + } + if (debug) + { + System.err.println("Returning empty '" + separator + + "' separated List\n"); + } + return "" + separator; + } + + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups() + */ + public String 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 (stn.toLowerCase().equals("true")) + { + 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; + } + + /** + * return the given colour value parameter or the given default if parameter + * not given + * + * @param colparam + * @param defcolour + * @return + */ + public Color getDefaultColourParameter(String colparam, Color defcolour) + { + String colprop = getParameter(colparam); + if (colprop == null || colprop.trim().length() == 0) + { + return defcolour; + } + Color col = 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() + { + 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) + { + 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; } + */ }