X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=e177a59b7c31806772c5f2feb4aa944d463f56e1;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=393476d387131208575cc85fc0036c30ba98af32;hpb=f533fb6976a511f5e76afdf176fce0f5c580064d;p=jalview.git diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java old mode 100755 new mode 100644 index 393476d..e177a59 --- a/src/jalview/bin/JalviewLite.java +++ b/src/jalview/bin/JalviewLite.java @@ -1,92 +1,145 @@ /* - * 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 2.9.0b2) + * 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.javascript.MouseOverStructureListener; +import jalview.structure.SelectionListener; +import jalview.structure.StructureSelectionManager; +import jalview.util.HttpUtils; +import jalview.util.MessageManager; + +import java.applet.Applet; +import java.awt.Button; +import java.awt.Color; +import java.awt.Component; +import java.awt.EventQueue; +import java.awt.Font; +import java.awt.Frame; +import java.awt.Graphics; +import java.awt.event.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.ArrayList; +import java.util.Hashtable; +import java.util.List; +import java.util.StringTokenizer; +import java.util.Vector; + +import netscape.javascript.JSObject; /** * Jalview Applet. Runs in Java 1.18 runtime * * @author $author$ - * @version $Revision$ + * @version $Revision: 1.92 $ */ -public class JalviewLite extends Applet +public class JalviewLite extends Applet implements + StructureSelectionManagerProvider, JalviewLiteJsApi { + private static final String TRUE = "true"; + + private static final String FALSE = "false"; + + public StructureSelectionManager getStructureSelectionManager() + { + return StructureSelectionManager.getStructureSelectionManager(this); + } + // ///////////////////////////////////////// - // The following public methods maybe called + // The following public methods may be called // externally, eg via javascript in HTML page - /** - * @return String list of selected sequence IDs, each terminated by "¬" - * (¬) + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences() */ public String getSelectedSequences() { return getSelectedSequencesFrom(getDefaultTargetFrame()); } - /** - * @param sep - * separator string or null for default - * @return String list of selected sequence IDs, each terminated by sep or - * ("¬" as default) + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String) */ public String getSelectedSequences(String sep) { return getSelectedSequencesFrom(getDefaultTargetFrame(), sep); } - /** - * @param alf - * alignframe containing selection - * @return String list of selected sequence IDs, each terminated by "¬" + /* + * (non-Javadoc) * + * @see + * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui + * .AlignFrame) */ public String getSelectedSequencesFrom(AlignFrame alf) { - return getSelectedSequencesFrom(alf, "¬"); + return getSelectedSequencesFrom(alf, separator); // ""+0x00AC); } - /** - * get list of selected sequence IDs separated by given separator + /* + * (non-Javadoc) * - * @param alf - * window containing selection - * @param sep - * separator string to use - default is "¬" - * @return String list of selected sequence IDs, each terminated by the given - * separator + * @see + * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui + * .AlignFrame, java.lang.String) */ public String getSelectedSequencesFrom(AlignFrame alf, String sep) { StringBuffer result = new StringBuffer(""); if (sep == null || sep.length() == 0) { - sep = "¬"; + sep = separator; // "+0x00AC; } if (alf.viewport.getSelectionGroup() != null) { @@ -103,46 +156,360 @@ public class JalviewLite extends Applet return result.toString(); } - /** - * get sequences selected in current alignFrame and return their alignment in - * format 'format' either with or without suffix - * - * @param alf - - * where selection is - * @param format - - * format of alignment file - * @param suffix - - * "true" to append /start-end string to each sequence ID - * @return selected sequences as flat file or empty string if there was no - * current selection + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#highlight(java.lang.String, + * java.lang.String, java.lang.String) + */ + public void highlight(String sequenceId, String position, + String alignedPosition) + { + highlightIn(getDefaultTargetFrame(), sequenceId, position, + alignedPosition); + } + + /* + * (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) + { + // 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); + } + }); + } + } + } + + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String, + * java.lang.String) + */ + public void select(String sequenceIds, String columns) + { + selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator); + } + + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String, + * java.lang.String, java.lang.String) + */ + public void select(String sequenceIds, String columns, String sep) + { + selectIn(getDefaultTargetFrame(), sequenceIds, columns, sep); + } + + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame, + * java.lang.String, java.lang.String) + */ + public void selectIn(AlignFrame alf, String sequenceIds, String columns) + { + selectIn(alf, sequenceIds, columns, separator); + } + + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame, + * java.lang.String, java.lang.String, java.lang.String) + */ + public void selectIn(final AlignFrame alf, String sequenceIds, + String columns, String sep) + { + if (sep == null || sep.length() == 0) + { + sep = separator; + } + else + { + if (debug) + { + System.err.println("Selecting region using separator string '" + + separator + "'"); + } + } + // deparse fields + String[] ids = separatorListToArray(sequenceIds, sep); + String[] cols = separatorListToArray(columns, sep); + 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); + } + }); + } + } + + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignment(java.lang. + * String, java.lang.String) */ public String getSelectedSequencesAsAlignment(String format, String suffix) { - return getSelectedSequencesAsAlignmentFrom(currentAlignFrame, format, - suffix); + return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(), + format, suffix); } - /** - * get sequences selected in alf and return their alignment in format 'format' - * either with or without suffix - * - * @param alf - - * where selection is - * @param format - - * format of alignment file - * @param suffix - - * "true" to append /start-end string to each sequence ID - * @return selected sequences as flat file or empty string if there was no - * current selection + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignmentFrom(jalview + * .appletgui.AlignFrame, java.lang.String, java.lang.String) */ public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, String format, String suffix) { try { - boolean seqlimits = suffix.equalsIgnoreCase("true"); + boolean seqlimits = suffix.equalsIgnoreCase(TRUE); if (alf.viewport.getSelectionGroup() != null) { + // JBPNote: getSelectionAsNewSequence behaviour has changed - this + // method now returns a full copy of sequence data + // TODO consider using getSequenceSelection instead here String reply = new AppletFormatAdapter().formatSequences(format, new Alignment(alf.viewport.getSelectionAsNewSequence()), seqlimits); @@ -156,27 +523,172 @@ public class JalviewLite extends Applet return ""; } + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder() + */ + public String getAlignmentOrder() + { + return getAlignmentOrderFrom(getDefaultTargetFrame()); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame + * ) + */ + public String getAlignmentOrderFrom(AlignFrame alf) + { + return getAlignmentOrderFrom(alf, separator); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame + * , java.lang.String) + */ + public String getAlignmentOrderFrom(AlignFrame alf, String sep) + { + AlignmentI alorder = alf.getAlignViewport().getAlignment(); + String[] order = new String[alorder.getHeight()]; + for (int i = 0; i < order.length; i++) + { + order[i] = alorder.getSequenceAt(i).getName(); + } + return arrayToSeparatorList(order); + } + + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String, + * java.lang.String) + */ + public String orderBy(String order, String undoName) + { + return orderBy(order, undoName, separator); + } + + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String, + * java.lang.String, java.lang.String) + */ + public String orderBy(String order, String undoName, String sep) + { + return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#orderAlignmentBy(jalview.appletgui.AlignFrame, + * java.lang.String, java.lang.String, java.lang.String) + */ + public String orderAlignmentBy(AlignFrame alf, String order, + String undoName, String sep) + { + String[] ids = separatorListToArray(order, sep); + SequenceI[] sqs = null; + if (ids != null && ids.length > 0) + { + jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher( + alf.viewport.getAlignment().getSequencesArray()); + int s = 0; + sqs = new SequenceI[ids.length]; + for (int i = 0; i < ids.length; i++) + { + if (ids[i].trim().length() == 0) + { + continue; + } + SequenceI sq = matcher.findIdMatch(ids[i]); + if (sq != null) + { + sqs[s++] = sq; + } + } + if (s > 0) + { + SequenceI[] sqq = new SequenceI[s]; + System.arraycopy(sqs, 0, sqq, 0, s); + sqs = sqq; + } + else + { + sqs = null; + } + } + if (sqs == null) + { + return ""; + } + ; + final AlignmentOrder aorder = new AlignmentOrder(sqs); + + if (undoName != null && undoName.trim().length() == 0) + { + undoName = null; + } + final String _undoName = undoName; + // TODO: deal with synchronization here: cannot raise any events until after + // this has returned. + return alf.sortBy(aorder, _undoName) ? TRUE : ""; + } + + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String) + */ public String getAlignment(String format) { - return getAlignmentFrom(getDefaultTargetFrame(), format, "true"); + 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"); + return getAlignmentFrom(alf, format, TRUE); } + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String, + * java.lang.String) + */ public String getAlignment(String format, String suffix) { return getAlignmentFrom(getDefaultTargetFrame(), format, suffix); } + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame, + * java.lang.String, java.lang.String) + */ public String getAlignmentFrom(AlignFrame alf, String format, String suffix) { try { - boolean seqlimits = suffix.equalsIgnoreCase("true"); + boolean seqlimits = suffix.equalsIgnoreCase(TRUE); String reply = new AppletFormatAdapter().formatSequences(format, alf.viewport.getAlignment(), seqlimits); @@ -188,15 +700,27 @@ public class JalviewLite extends Applet } } + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String) + */ public void loadAnnotation(String annotation) { loadAnnotationFrom(getDefaultTargetFrame(), annotation); } + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame + * , java.lang.String) + */ public void loadAnnotationFrom(AlignFrame alf, String annotation) { - if (new AnnotationFile().readAnnotationFile(alf.getAlignViewport() - .getAlignment(), annotation, AppletFormatAdapter.PASTE)) + if (new AnnotationFile().annotateAlignmentView(alf.getAlignViewport(), + annotation, AppletFormatAdapter.PASTE)) { alf.alignPanel.fontChanged(); alf.alignPanel.setScrollValues(0, 0); @@ -207,57 +731,125 @@ public class JalviewLite extends Applet } } + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String) + */ + public void loadFeatures(String features, boolean autoenabledisplay) + { + loadFeaturesFrom(getDefaultTargetFrame(), features, autoenabledisplay); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame + * , java.lang.String) + */ + public boolean loadFeaturesFrom(AlignFrame alf, String features, + boolean autoenabledisplay) + { + return alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE, + autoenabledisplay); + } + + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String) + */ public String getFeatures(String format) { return getFeaturesFrom(getDefaultTargetFrame(), format); } + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame, + * java.lang.String) + */ public String getFeaturesFrom(AlignFrame alf, String format) { return alf.outputFeatures(false, format); } + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#getAnnotation() + */ public String getAnnotation() { return getAnnotationFrom(getDefaultTargetFrame()); } + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame + * ) + */ public String getAnnotationFrom(AlignFrame alf) { return alf.outputAnnotations(false); } + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#newView() + */ public AlignFrame newView() { return newViewFrom(getDefaultTargetFrame()); } + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String) + */ public AlignFrame newView(String name) { return newViewFrom(getDefaultTargetFrame(), name); } + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame) + */ public AlignFrame newViewFrom(AlignFrame alf) { return alf.newView(null); } + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame, + * java.lang.String) + */ public AlignFrame newViewFrom(AlignFrame alf, String name) { return alf.newView(name); } - /** + /* + * (non-Javadoc) * - * @param text - * alignment file as a string - * @param title - * window title - * @return null or new alignment frame + * @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String, + * java.lang.String) */ public AlignFrame loadAlignment(String text, String title) { - Alignment al = null; + AlignmentI al = null; + String format = new IdentifyFile().Identify(text, AppletFormatAdapter.PASTE); try @@ -275,18 +867,391 @@ public class JalviewLite extends Applet return null; } - // ////////////////////////////////////////////// + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String) + */ + public void setMouseoverListener(String listener) + { + setMouseoverListener(currentAlignFrame, listener); + } + + private Vector 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."); + } + } + + /** + * Callable from javascript to register a javascript function to pass events + * to a structure viewer. + * + * @param listener + * the name of a javascript function + * @param modelSet + * a token separated list of PDB file names listened for + * @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String, + * java.lang.String) + */ + public void setStructureListener(String listener, String modelSet) + { + if (listener != null) + { + listener = listener.trim(); + if (listener.length() == 0) + { + System.err + .println("jalview Javascript error: Ignoring empty function for selection listener."); + return; + } + } + MouseOverStructureListener mol = new MouseOverStructureListener(this, + listener, separatorListToArray(modelSet)); + javascriptListeners.addElement(mol); + StructureSelectionManager.getStructureSelectionManager(this) + .addStructureViewerListener(mol); + if (debug) + { + System.err.println("Added a javascript structure viewer listener '" + + listener + "'"); + System.err.println("There are now " + javascriptListeners.size() + + " listeners in total."); + } + } + + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui + * .AlignFrame, java.lang.String) + */ + 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(); + } + } + }); + + } + + // ////////////////////////////////////////////// // ////////////////////////////////////////////// - static int lastFrameX = 200; + public static int lastFrameX = 200; - static int lastFrameY = 200; + public static int lastFrameY = 200; boolean fileFound = true; String file = "No file"; - Button launcher = new Button("Start Jalview"); + String file2 = null; + + Button launcher = new Button( + MessageManager.getString("label.start_jalview")); /** * The currentAlignFrame is static, it will change if and when the user @@ -294,42 +1259,143 @@ public class JalviewLite extends Applet * AlignFrame if the applet is started as embedded on the page and then * afterwards a new view is created. */ - public static AlignFrame currentAlignFrame; + public AlignFrame currentAlignFrame = null; /** * This is the first frame to be displayed, and does not change. API calls * will default to this instance if currentAlignFrame is null. */ - AlignFrame initialAlignFrame; + AlignFrame initialAlignFrame = null; boolean embedded = false; private boolean checkForJmol = true; + private boolean checkedForJmol = false; // ensure we don't check for jmol + + // every time the app is re-inited + public boolean jmolAvailable = false; - public static boolean debug; + 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 */ + @Override public void init() { - /** - * turn on extra applet debugging - */ - String dbg = getParameter("debug"); - if (dbg != null) + debug = TRUE.equalsIgnoreCase(getParameter("debug")); + try { - debug = dbg.toLowerCase().equals("true"); + if (debug) + { + System.err.println("Applet context is '" + + getAppletContext().getClass().toString() + "'"); + } + JSObject scriptObject = JSObject.getWindow(this); + if (debug && scriptObject != null) + { + System.err.println("Applet has Javascript callback support."); + } + + } catch (Exception ex) + { + System.err + .println("Warning: No JalviewLite javascript callbacks available."); + if (debug) + { + ex.printStackTrace(); + } + } + + if (debug) + { + System.err.println("JalviewLite Version " + getVersion()); + System.err.println("Build Date : " + getBuildDate()); + System.err.println("Installation : " + getInstallation()); + } + String externalsviewer = getParameter("externalstructureviewer"); + if (externalsviewer != null) + { + useXtrnalSviewer = externalsviewer.trim().toLowerCase().equals(TRUE); } /** * if true disable the check for jmol */ String chkforJmol = getParameter("nojmol"); - if (chkforJmol!=null) + if (chkforJmol != null) { - checkForJmol = !chkforJmol.equals("true"); + checkForJmol = !chkforJmol.equals(TRUE); } /** * get the separator parameter if present @@ -348,7 +1414,8 @@ public class JalviewLite extends Applet else { throw new Error( - "Invalid separator parameter - must be non-zero length"); + MessageManager + .getString("error.invalid_separator_parameter")); } } int r = 255; @@ -370,14 +1437,13 @@ public class JalviewLite extends Applet b = 255; } } - param = getParameter("label"); if (param != null) { launcher.setLabel(param); } - this.setBackground(new Color(r, g, b)); + setBackground(new Color(r, g, b)); file = getParameter("file"); @@ -396,41 +1462,40 @@ public class JalviewLite extends Applet file = data.toString(); } } + if (getDefaultParameter("enableSplitFrame", true)) + { + file2 = getParameter("file2"); + } - LoadJmolThread jmolAvailable = new LoadJmolThread(); - jmolAvailable.start(); - - final JalviewLite applet = this; - if (getParameter("embedded") != null - && getParameter("embedded").equalsIgnoreCase("true")) + embedded = TRUE.equalsIgnoreCase(getParameter("embedded")); + if (embedded) { - // Launch as embedded applet in page - embedded = true; - LoadingThread loader = new LoadingThread(file, applet); + LoadingThread loader = new LoadingThread(file, file2, this); loader.start(); } else if (file != null) { - if (getParameter("showbutton") == null - || !getParameter("showbutton").equalsIgnoreCase("false")) + /* + * Start the applet immediately or show a button to start it + */ + if (FALSE.equalsIgnoreCase(getParameter("showbutton"))) + { + LoadingThread loader = new LoadingThread(file, file2, this); + loader.start(); + } + else { - // Add the JalviewLite 'Button' to the page add(launcher); launcher.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - LoadingThread loader = new LoadingThread(file, applet); + LoadingThread loader = new LoadingThread(file, file2, + JalviewLite.this); loader.start(); } }); } - else - { - // Open jalviewLite immediately. - LoadingThread loader = new LoadingThread(file, applet); - loader.start(); - } } else { @@ -438,6 +1503,88 @@ public class JalviewLite extends Applet // still be called to open new alignments. file = "NO FILE"; fileFound = false; + callInitCallback(); + } + } + + private void initLiveConnect() + { + // try really hard to get the liveConnect thing working + boolean notFailed = false; + int tries = 0; + while (!notFailed && tries < 10) + { + if (tries > 0) + { + System.err.println("LiveConnect request thread going to sleep."); + } + try + { + Thread.sleep(700 * (1 + tries)); + } catch (InterruptedException q) + { + } + ; + if (tries++ > 0) + { + System.err.println("LiveConnect request thread woken up."); + } + try + { + JSObject scriptObject = JSObject.getWindow(this); + if (scriptObject.eval("navigator") != null) + { + notFailed = true; + } + } catch (Exception jsex) + { + System.err.println("Attempt " + tries + + " to access LiveConnect javascript failed."); + } + } + } + + private void callInitCallback() + { + String initjscallback = getParameter("oninit"); + if (initjscallback == null) + { + return; + } + initjscallback = initjscallback.trim(); + if (initjscallback.length() > 0) + { + JSObject scriptObject = null; + try + { + scriptObject = JSObject.getWindow(this); + } catch (Exception ex) + { + } + ; + // try really hard to let the browser plugin know we want liveconnect + initLiveConnect(); + + if (scriptObject != null) + { + try + { + // do onInit with the JS executor thread + new JSFunctionExec(this).executeJavascriptFunction(true, + initjscallback, null, "Calling oninit callback '" + + initjscallback + "'."); + } catch (Exception e) + { + System.err.println("Exception when executing _oninit callback '" + + initjscallback + "'."); + e.printStackTrace(); + } + } + else + { + System.err.println("Not executing _oninit callback '" + + initjscallback + "' - no scripting allowed."); + } } } @@ -445,13 +1592,13 @@ public class JalviewLite extends Applet * Initialises and displays a new java.awt.Frame * * @param frame - * java.awt.Frame to be displayed + * java.awt.Frame to be displayed * @param title - * title of new frame + * title of new frame * @param width - * width if new frame + * width if new frame * @param height - * height of new frame + * height of new frame */ public static void addFrame(final Frame frame, String title, int width, int height) @@ -467,11 +1614,15 @@ public class JalviewLite extends Applet { if (frame instanceof AlignFrame) { + AlignViewport vp = ((AlignFrame) frame).viewport; ((AlignFrame) frame).closeMenuItem_actionPerformed(); - } - if (currentAlignFrame == frame) - { - currentAlignFrame = null; + if (vp.applet.currentAlignFrame == frame) + { + vp.applet.currentAlignFrame = null; + } + vp.applet = null; + vp = null; + } lastFrameX -= 40; lastFrameY -= 40; @@ -487,7 +1638,7 @@ public class JalviewLite extends Applet { if (frame instanceof AlignFrame) { - currentAlignFrame = (AlignFrame) frame; + ((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame; if (debug) { System.err.println("Activated window " + frame); @@ -499,7 +1650,9 @@ public class JalviewLite extends Applet /* * Probably not necessary to do this - see TODO above. (non-Javadoc) * - * @see java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent) + * @see + * java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent + * ) * * public void windowDeactivated(WindowEvent e) { if (currentAlignFrame == * frame) { currentAlignFrame = null; if (debug) { @@ -516,7 +1669,7 @@ public class JalviewLite extends Applet * If file given in parameter not found, displays error message * * @param g - * graphics context + * graphics context */ public void paint(Graphics g) { @@ -526,22 +1679,56 @@ public class JalviewLite extends Applet g.setColor(Color.cyan); g.fillRect(0, 0, getSize().width, getSize().height); g.setColor(Color.red); - g.drawString("Jalview can't open file", 5, 15); + g.drawString( + MessageManager.getString("label.jalview_cannot_open_file"), + 5, 15); g.drawString("\"" + file + "\"", 5, 30); } else if (embedded) { g.setColor(Color.black); g.setFont(new Font("Arial", Font.BOLD, 24)); - g.drawString("Jalview Applet", 50, this.getSize().height / 2 - 30); - g.drawString("Loading Data...", 50, this.getSize().height / 2); + g.drawString(MessageManager.getString("label.jalview_applet"), 50, + getSize().height / 2 - 30); + g.drawString(MessageManager.getString("label.loading_data") + "...", + 50, getSize().height / 2); } } + /** + * get all components associated with the applet of the given type + * + * @param class1 + * @return + */ + public Vector getAppletWindow(Class class1) + { + Vector wnds = new Vector(); + Component[] cmp = getComponents(); + if (cmp != null) + { + for (int i = 0; i < cmp.length; i++) + { + if (class1.isAssignableFrom(cmp[i].getClass())) + { + wnds.addElement(cmp); + } + } + } + return wnds; + } + class LoadJmolThread extends Thread { + private boolean running = false; + public void run() { + if (running || checkedForJmol) + { + return; + } + running = true; if (checkForJmol) { try @@ -559,38 +1746,42 @@ public class JalviewLite extends Applet } catch (java.lang.ClassNotFoundException ex) { } - } else { - jmolAvailable=false; + } + else + { + jmolAvailable = false; if (debug) { - System.err.println("Skipping Jmol check. Will use MCView (probably)"); + 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; // alignment file or URL spec + + String _file2; // second alignment file or URL spec JalviewLite applet; private void dbgMsg(String msg) { - if (applet.debug) + if (JalviewLite.debug) { System.err.println(msg); } @@ -600,351 +1791,623 @@ public class JalviewLite extends Applet * update the protocol state variable for accessing the datasource located * by file. * - * @param file + * @param path * @return possibly updated datasource string */ - public String setProtocolState(String file) + public String resolveFileProtocol(String path) { - if (file.startsWith("PASTE")) + /* + * is it paste data? + */ + if (path.startsWith("PASTE")) { - file = file.substring(5); protocol = AppletFormatAdapter.PASTE; + return path.substring(5); } - else if (inArchive(file)) + + /* + * is it a URL? + */ + if (path.indexOf("://") != -1) { - protocol = AppletFormatAdapter.CLASSLOADER; + protocol = AppletFormatAdapter.URL; + return path; } - else + + /* + * try relative to document root + */ + URL documentBase = getDocumentBase(); + String withDocBase = resolveUrlForLocalOrAbsolute(path, documentBase); + if (HttpUtils.isValidUrl(withDocBase)) + { + if (debug) + { + System.err.println("Prepended document base '" + documentBase + + "' to make: '" + withDocBase + "'"); + } + protocol = AppletFormatAdapter.URL; + return withDocBase; + } + + /* + * try relative to codebase (if different to document base) + */ + URL codeBase = getCodeBase(); + String withCodeBase = applet.resolveUrlForLocalOrAbsolute(path, + codeBase); + if (!withCodeBase.equals(withDocBase) + && HttpUtils.isValidUrl(withCodeBase)) { - file = addProtocol(file); protocol = AppletFormatAdapter.URL; + if (debug) + { + System.err.println("Prepended codebase '" + codeBase + + "' to make: '" + withCodeBase + "'"); + } + return withCodeBase; + } + + /* + * try locating by classloader; try this last so files in the directory + * are resolved using document base + */ + if (inArchive(path)) + { + protocol = AppletFormatAdapter.CLASSLOADER; } - dbgMsg("Protocol identified as '" + protocol + "'"); - return file; + return path; } - public LoadingThread(String _file, JalviewLite _applet) + public LoadingThread(String file, String file2, JalviewLite _applet) { - 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 + "'"); + 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() { + dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile"); + dbgMsg("Loading started."); - Alignment al = null; - try - { - al = new AppletFormatAdapter().readFile(file, protocol, format); - } catch (java.io.IOException ex) + + AlignFrame newAlignFrame = readAlignment(_file); + AlignFrame newAlignFrame2 = readAlignment(_file2); + if (newAlignFrame != null) { - dbgMsg("File load exception."); - ex.printStackTrace(); + addToDisplay(newAlignFrame, newAlignFrame2); + loadTree(newAlignFrame); + + loadScoreFile(newAlignFrame); + + loadFeatures(newAlignFrame); + + loadAnnotations(newAlignFrame); + + loadJnetFile(newAlignFrame); + + loadPdbFiles(newAlignFrame); } - if ((al != null) && (al.getHeight() > 0)) + else { - dbgMsg("Successfully loaded file."); - initialAlignFrame = new AlignFrame(al, applet, file, embedded); - // update the focus. - currentAlignFrame = initialAlignFrame; + fileFound = false; + applet.remove(launcher); + applet.repaint(); + } + 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(); + AlignmentI cdna = al1.isNucleotide() ? al1 : al2; + AlignmentI prot = al1.isNucleotide() ? al2 : al1; + if (AlignmentUtils.mapProteinAlignmentToCdna(prot, cdna)) { - currentAlignFrame.setTitle("Sequences from " + getDocumentBase()); + al2.alignAs(al1); + SplitFrame sf = new SplitFrame(af, af2); + sf.addToDisplay(embedded, JalviewLite.this); + return; } + else + { + String msg = "Could not map any sequence in " + af2.getTitle() + + " as " + + (al1.isNucleotide() ? "protein product" : "cDNA") + + " for " + af.getTitle(); + System.err.println(msg); + } + } - currentAlignFrame.statusBar.setText("Successfully loaded file " - + file); + af.addToDisplay(embedded); + } - String treeFile = applet.getParameter("tree"); - 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 = resolveFileProtocol(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)) { - treeFile = applet.getParameter("treeFile"); - } + dbgMsg("Successfully loaded file."); + al.setDataset(null); + AlignFrame newAlignFrame = new AlignFrame(al, applet, + resolvedFile, embedded, false); + newAlignFrame.setTitle(resolvedFile); + if (initialAlignFrame == null) + { + initialAlignFrame = newAlignFrame; + } + // update the focus. + currentAlignFrame = newAlignFrame; + + if (protocol == AppletFormatAdapter.PASTE) + { + newAlignFrame.setTitle(MessageManager.formatMessage( + "label.sequences_from", new Object[] { applet + .getDocumentBase().toString() })); + } - if (treeFile != null) + newAlignFrame.statusBar.setText(MessageManager.formatMessage( + "label.successfully_loaded_file", + new Object[] { resolvedFile })); + + return newAlignFrame; + } + } catch (java.io.IOException ex) + { + dbgMsg("File load exception."); + ex.printStackTrace(); + if (debug) { try { - treeFile = setProtocolState(treeFile); - /* - * if (inArchive(treeFile)) { protocol = - * AppletFormatAdapter.CLASSLOADER; } else { protocol = - * AppletFormatAdapter.URL; treeFile = addProtocol(treeFile); } - */ - jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile, - protocol); - - fin.parse(); - - if (fin.getTree() != null) - { - currentAlignFrame.loadTree(fin, treeFile); - dbgMsg("Successfuly imported tree."); - } - else + FileParse fp = new FileParse(resolvedFile, protocol); + String ln = null; + dbgMsg(">>>Dumping contents of '" + resolvedFile + "' " + "(" + + protocol + ")"); + while ((ln = fp.nextLine()) != null) { - dbgMsg("Tree parameter did not resolve to a valid tree."); + 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) - { - param = setProtocolState(param); + /** + * 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 + */ - currentAlignFrame.parseFeaturesFile(param, protocol); - } + applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles", + false)); + /* + * + * + * + * + * + */ - param = getParameter("showFeatureSettings"); - if (param != null && param.equalsIgnoreCase("true")) + 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) { - currentAlignFrame.viewport.showSequenceFeatures(true); - new FeatureSettings(currentAlignFrame.alignPanel); + param = applet.getParameter("PDBFILE" + pdbFileCount); } - - param = getParameter("annotations"); - if (param != null) + else { - param = setProtocolState(param); - - if (new AnnotationFile().readAnnotationFile( - currentAlignFrame.viewport.getAlignment(), param, - protocol)) - { - currentAlignFrame.alignPanel.fontChanged(); - currentAlignFrame.alignPanel.setScrollValues(0, 0); - } - else - { - System.err - .println("Annotations were not added from annotation file '" - + param + "'"); - } - + param = applet.getParameter("PDBFILE"); } - param = getParameter("jnetfile"); if (param != null) { - try - { - param = setProtocolState(param); - jalview.io.JPredFile predictions = new jalview.io.JPredFile( - param, protocol); - JnetAnnotationMaker.add_annotation(predictions, - currentAlignFrame.viewport.getAlignment(), 0, false); // false==do - // not - // add - // sequence - // profile - // from - // concise - // output - currentAlignFrame.alignPanel.fontChanged(); - currentAlignFrame.alignPanel.setScrollValues(0, 0); - } catch (Exception ex) - { - ex.printStackTrace(); - } - } + PDBEntry pdb = new PDBEntry(); - /* - * - * - * - * - * - */ + String seqstring; + SequenceI[] seqs = null; + String[] chains = null; - int pdbFileCount = 0; - do - { - if (pdbFileCount > 0) - param = getParameter("PDBFILE" + pdbFileCount); - else - param = getParameter("PDBFILE"); + StringTokenizer st = new StringTokenizer(param, " "); - if (param != null) + if (st.countTokens() < 2) { - 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) { - String sequence = applet.getParameter("PDBSEQ"); - if (sequence != null) - seqs = new SequenceI[] - { (Sequence) currentAlignFrame.getAlignViewport() - .getAlignment().findName(sequence) }; - + seqs = new SequenceI[] { matcher == null ? (Sequence) alignFrame + .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((Sequence) currentAlignFrame - .getAlignViewport().getAlignment().findName( - seqstring)); - } + } + else + { + param = st.nextToken(); + List tmp = new ArrayList(); + List tmp2 = new ArrayList(); - seqs = new SequenceI[tmp.size()]; - tmp.copyInto(seqs); - if (tmp2.size() == tmp.size()) + while (st.hasMoreTokens()) + { + seqstring = st.nextToken(); + StringTokenizer st2 = new StringTokenizer(seqstring, "="); + if (st2.countTokens() > 1) { - chains = new String[tmp2.size()]; - tmp2.copyInto(chains); + // This is the chain + tmp2.add(st2.nextToken()); + seqstring = st2.nextToken(); } + tmp.add(matcher == null ? (Sequence) alignFrame + .getAlignViewport().getAlignment() + .findName(seqstring) : matcher.findIdMatch(seqstring)); } - param = setProtocolState(param); - if (!jmolAvailable - && protocol == AppletFormatAdapter.CLASSLOADER) + seqs = tmp.toArray(new SequenceI[tmp.size()]); + if (tmp2.size() == tmp.size()) { - // TODO: pass PDB file in classloader on to Jmol - // This exception preserves the current behaviour where, even if - // the local pdb file was identified in the class loader - protocol = AppletFormatAdapter.URL; // this is probably NOT - // CORRECT! - param = addProtocol(param); // + chains = tmp2.toArray(new String[tmp2.size()]); } + } + param = resolveFileProtocol(param); + // TODO check JAL-357 for files in a jar (CLASSLOADER) + pdb.setFile(param); - pdb.setFile(param); - - if (seqs != null) + if (seqs != null) + { + for (int i = 0; i < seqs.length; i++) { - for (int i = 0; i < seqs.length; i++) + if (seqs[i] != null) { - if (seqs[i] != null) - { - ((Sequence) seqs[i]).addPDBId(pdb); - } - else + ((Sequence) seqs[i]).addPDBId(pdb); + StructureSelectionManager.getStructureSelectionManager( + applet).registerPDBEntry(pdb); + } + else + { + if (JalviewLite.debug) { - 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 + ")"); - } + // this may not really be a problem but we give a warning + // anyway + System.err + .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence " + + i + ")"); } } + } + + if (!alignPdbStructures) + { + alignFrame.newStructureView(applet, pdb, seqs, chains, + protocol); + } + else + { + pdbs.addElement(new Object[] { pdb, seqs, chains, + new String(protocol) }); + } + } + } + + pdbFileCount++; + } while (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; + } + + /** + * Load in a Jnetfile if specified by parameter. Returns true if loaded, + * else false. + * + * @param alignFrame + * @return + */ + protected boolean loadJnetFile(AlignFrame alignFrame) + { + boolean result = false; + String param = applet.getParameter("jnetfile"); + if (param != null) + { + try + { + param = resolveFileProtocol(param); + JPredFile predictions = new JPredFile(param, protocol); + JnetAnnotationMaker.add_annotation(predictions, + alignFrame.viewport.getAlignment(), 0, false); + // false == do not add sequence profile from concise output + SequenceI repseq = alignFrame.viewport.getAlignment() + .getSequenceAt(0); + alignFrame.viewport.getAlignment().setSeqrep(repseq); + ColumnSelection cs = new ColumnSelection(); + cs.hideInsertionsFor(repseq); + alignFrame.viewport.setColumnSelection(cs); + alignFrame.alignPanel.fontChanged(); + alignFrame.alignPanel.setScrollValues(0, 0); + result = true; + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + return result; + } + + /** + * Load annotations if specified by parameter. Returns true if loaded, else + * false. + * + * @param alignFrame + * @return + */ + protected boolean loadAnnotations(AlignFrame alignFrame) + { + boolean result = false; + String param = applet.getParameter("annotations"); + if (param != null) + { + param = resolveFileProtocol(param); + + if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport, + param, protocol)) + { + alignFrame.alignPanel.fontChanged(); + alignFrame.alignPanel.setScrollValues(0, 0); + result = true; + } + else + { + System.err + .println("Annotations were not added from annotation file '" + + param + "'"); + } + } + 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 = resolveFileProtocol(param); - 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); - } - } + result = alignFrame.parseFeaturesFile(param, protocol); + } - pdbFileCount++; - } while (pdbFileCount < 10); + param = applet.getParameter("showFeatureSettings"); + if (param != null && param.equalsIgnoreCase(TRUE)) + { + alignFrame.viewport.setShowSequenceFeatures(true); + new FeatureSettings(alignFrame.alignPanel); + } + return result; + } - // /////////////////////////// - // modify display of features - // - // hide specific groups - param = getParameter("hidefeaturegroups"); - if (param != null) + /** + * 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 { - applet.setFeatureGroupState(param, false); - } - // show specific groups - param = getParameter("showfeaturegroups"); - if (param != null) + 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) { - applet.setFeatureGroupState(param, true); + System.err.printf("Cannot read score file: '%s'. Cause: %s \n", + sScoreFile, e.getMessage()); } } - else + 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) { - fileFound = false; - remove(launcher); - repaint(); + treeFile = applet.getParameter("treeFile"); + } + + if (treeFile != null) + { + try + { + treeFile = resolveFileProtocol(treeFile); + NewickFile fin = new NewickFile(treeFile, protocol); + fin.parse(); + + if (fin.getTree() != null) + { + alignFrame.loadTree(fin, treeFile); + result = true; + dbgMsg("Successfully imported tree."); + } + else + { + dbgMsg("Tree parameter did not resolve to a valid tree."); + } + } catch (Exception ex) + { + ex.printStackTrace(); + } } + return result; } /** * Discovers whether the given file is in the Applet Archive * - * @param file - * String + * @param f + * String * @return boolean */ - boolean inArchive(String file) + boolean inArchive(String f) { // This might throw a security exception in certain browsers // Netscape Communicator for instance. try { - boolean rtn = (getClass().getResourceAsStream("/" + file) != null); + boolean rtn = (getClass().getResourceAsStream("/" + f) != null); if (debug) { - System.err.println("Resource '" + file + "' was " - + (rtn ? "" : "not") + " located by classloader."); + System.err.println("Resource '" + f + "' was " + + (rtn ? "" : "not ") + "located by classloader."); } return rtn; } catch (Exception ex) { - System.out.println("Exception checking resources: " + file + " " - + ex); + System.out.println("Exception checking resources: " + f + " " + ex); return false; } } - - String addProtocol(String file) - { - if (file.indexOf("://") == -1) - { - file = getCodeBase() + file; - if (debug) - { - System.err.println("Prepended codebase for resource: '" + file - + "'"); - } - } - - return file; - } } /** @@ -952,7 +2415,7 @@ public class JalviewLite extends Applet * return null with an error message on System.err indicating the * fact. */ - protected AlignFrame getDefaultTargetFrame() + public AlignFrame getDefaultTargetFrame() { if (currentAlignFrame != null) { @@ -970,8 +2433,14 @@ public class JalviewLite extends Applet /** * separator used for separatorList */ - protected String separator = "|"; // this is a safe(ish) separator - tabs - // don't work for firefox + 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 @@ -981,9 +2450,24 @@ public class JalviewLite extends Applet */ 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 static String[] separatorListToArray(String list, String separator) + { + // TODO use StringUtils version (slightly different...) int seplen = separator.length(); - if (list == null || list.equals("")) + 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) @@ -993,7 +2477,11 @@ public class JalviewLite extends Applet } if (cp < list.length()) { - jv.addElement(list.substring(cp)); + String c = list.substring(cp); + if (!c.equals(separator)) + { + jv.addElement(c); + } } if (jv.size() > 0) { @@ -1030,20 +2518,32 @@ public class JalviewLite extends Applet */ public String arrayToSeparatorList(String[] list) { + return arrayToSeparatorList(list, separator); + } + + /** + * concatenate the list with separator + * + * @param list + * @param separator + * @return concatenated string + */ + public static String arrayToSeparatorList(String[] list, String separator) + { + // TODO use StringUtils version StringBuffer v = new StringBuffer(); - if (list != null) + if (list != null && list.length > 0) { - for (int i = 0, iSize = list.length - 1; i < iSize; i++) + for (int i = 0, iSize = list.length; i < iSize; i++) { if (list[i] != null) { + if (i > 0) + { + v.append(separator); + } v.append(list[i]); } - v.append(separator); - } - if (list[list.length - 1] != null) - { - v.append(list[list.length - 1]); } if (debug) { @@ -1058,12 +2558,13 @@ public class JalviewLite extends Applet 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() { @@ -1072,11 +2573,12 @@ public class JalviewLite extends Applet return lst; } - /** - * @param alf - * alignframe to get feature groups on - * @return - * @see jalview.appletgui.AlignFrame#getFeatureGroups() + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame + * ) */ public String getFeatureGroupsOn(AlignFrame alf) { @@ -1084,10 +2586,10 @@ public class JalviewLite extends Applet return lst; } - /** - * @param visible - * @return - * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean) + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean) */ public String getFeatureGroupsOfState(boolean visible) { @@ -1095,57 +2597,381 @@ public class JalviewLite extends Applet .getFeatureGroupsOfState(visible)); } - /** - * @param alf - * align frame to get groups of state visible - * @param visible - * @return - * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean) + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui + * .AlignFrame, boolean) */ public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible) { return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible)); } - /** - * @param groups - * tab separated list of group names - * @param state - * true or false - * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[], - * boolean) + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui. + * AlignFrame, java.lang.String, boolean) */ - public void setFeatureGroupStateOn(AlignFrame alf, String groups, - boolean state) + public void setFeatureGroupStateOn(final AlignFrame alf, + final String groups, boolean state) { - boolean st = state;// !(state==null || state.equals("") || - // state.toLowerCase().equals("false")); - alf.setFeatureGroupState(separatorListToArray(groups), st); + 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); } - /** - * List separator string + /* + * (non-Javadoc) * - * @return the separator + * @see jalview.bin.JalviewLiteJsApi#getSeparator() */ public String getSeparator() { return separator; } - /** - * List separator string + /* + * (non-Javadoc) * - * @param separator - * the separator to set + * @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String) */ public void setSeparator(String separator) { + if (separator == null || separator.length() < 1) + { + // reset to default + separator = "" + ((char) 0x00AC); + } this.separator = separator; + if (debug) + { + System.err.println("Default Separator now: '" + separator + "'"); + } + } + + /** + * 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; + } + + /** + * 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 targetPath + * - an absolute path on the same server as localref or a document + * located relative to localref + * @param localref + * - a URL on the same server as url + * @return a complete URL for the resource located by url + */ + private String resolveUrlForLocalOrAbsolute(String targetPath, + URL localref) + { + String resolvedPath = ""; + if (targetPath.startsWith("/")) + { + String codebase = localref.toString(); + String localfile = localref.getFile(); + resolvedPath = codebase.substring(0, + codebase.length() - localfile.length()) + + targetPath; + return resolvedPath; + } + + /* + * get URL path and strip off any trailing file e.g. + * www.jalview.org/examples/index.html#applets?a=b is trimmed to + * www.jalview.org/examples/ + */ + String urlPath = localref.toString(); + String directoryPath = urlPath; + int lastSeparator = directoryPath.lastIndexOf("/"); + if (lastSeparator > 0) + { + directoryPath = directoryPath.substring(0, lastSeparator + 1); + } + + if (targetPath.startsWith("/")) + { + /* + * construct absolute URL to a file on the server - this is not allowed? + */ + // String localfile = localref.getFile(); + // resolvedPath = urlPath.substring(0, + // urlPath.length() - localfile.length()) + // + targetPath; + resolvedPath = directoryPath + targetPath.substring(1); + } + else + { + resolvedPath = directoryPath + targetPath; + } + if (debug) + { + System.err.println("resolveUrlForLocalOrAbsolute returning " + + resolvedPath); + } + return resolvedPath; + } + + /** + * open a URL in the browser - resolving it according to relative refs and + * coping with javascript: protocol if necessary. + * + * @param url + * @param target + */ + public void showURL(String url, String target) + { + try + { + if (url.indexOf(":") == -1) + { + // TODO: verify (Bas Vroling bug) prepend codebase or server URL to + // form valid URL + // Should really use docbase, not codebase. + URL prepend; + url = resolveUrlForLocalOrAbsolute( + url, + prepend = getDefaultParameter("resolvetocodebase", false) ? getCodeBase() + : getDocumentBase()); + if (debug) + { + 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; } + */ }