/* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. * * 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 . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.bin; import jalview.analysis.SequenceIdMatcher; 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.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.AlignFile; import jalview.io.AnnotationFile; import jalview.io.AppletFormatAdapter; import jalview.io.FileParse; import jalview.io.IdentifyFile; import jalview.io.JnetAnnotationMaker; //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.JsSelectionSender; import jalview.javascript.MouseOverListener; import jalview.javascript.MouseOverStructureListener; import jalview.jsdev.GenericFileAdapter; //import jalview.javascript.MouseOverListener; //import jalview.javascript.MouseOverStructureListener; import jalview.schemes.ColourSchemeProperty; import jalview.schemes.UserColourScheme; import jalview.structure.SelectionListener; import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; import java.awt.Color; import java.awt.Component; import java.awt.EventQueue; import java.awt.Font; import java.awt.Graphics; import java.awt.event.ActionEvent; import java.awt.event.WindowAdapter; import java.awt.event.WindowEvent; import java.io.BufferedReader; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; import java.net.URL; import java.util.Hashtable; import java.util.List; import java.util.StringTokenizer; import java.util.Vector; import javax.swing.JApplet; import javax.swing.JButton; import javax.swing.JFrame; import netscape.javascript.JSObject; //import netscape.javascript.JSObject; /** * Jalview Applet. Runs in Java 1.18 runtime * * @author $author$ * @version $Revision: 1.92 $ */ public class JalviewLite extends JApplet implements StructureSelectionManagerProvider, JalviewLiteJsApi { private static final String TRUE = "true"; private static final String FALSE = "false"; public static boolean debug = false; public boolean embedded = false; public boolean enableSplitFrame = false; public boolean showButton = true; public boolean checkForJmol = true; public String jalviewServletURL; public String startupFile = "No file"; public String helpUrl; public String externalstructureviewer; public String sep; public String rgb; public String labelColour; public String initjscallback; public String pdbFile; public String sequence; public String jnetFile; public String annotations; public String hideFeatureGroups; public String showFeatureGroups; public String features; public String showFeatureSettings; public String scoreFile; public String treeFile; public String windowWidth; public String windowHeight; public String defaultColour; public String sortBy; public String wrap; public String centrecolumnlabels; public String userDefinedColour; public String widthScale; public String heightScale; public String upperCase; public String file2; private void setParams() { debug = TRUE.equalsIgnoreCase(getParameter("debug")); enableSplitFrame = TRUE.equalsIgnoreCase(getParameter("enableSplitFrame")); embedded = TRUE.equalsIgnoreCase(getParameter("embedded")); showButton = !FALSE.equalsIgnoreCase(getParameter("showbutton")); jalviewServletURL = getParameter("APPLICATION_URL"); startupFile = getParameter("file"); helpUrl = getParameter("jalviewhelpurl"); externalstructureviewer = getParameter("externalstructureviewer"); checkForJmol = !TRUE.equals(getParameter("nojmol")); sep = getParameter("separator"); rgb = getParameter("RGB"); labelColour = getParameter("label"); initjscallback = getParameter("oninit"); pdbFile = getParameter("PDBFILE"); sequence = getParameter("PDBSEQ"); jnetFile = getParameter("jnetfile"); annotations = getParameter("annotations"); hideFeatureGroups = getParameter("hidefeaturegroups"); showFeatureGroups = getParameter("showfeaturegroups"); features = getParameter("features"); showFeatureSettings = getParameter("showFeatureSettings"); scoreFile = getParameter("scoreFile"); treeFile = getParameter("tree"); if (treeFile == null) treeFile = getParameter("treeFile"); windowWidth = getParameter("windowWidth"); windowHeight = getParameter("windowHeight"); defaultColour = getParameter("defaultColour"); sortBy = getParameter("sortBy"); wrap = getParameter("wrap"); centrecolumnlabels = getParameter("centrecolumnlabels"); userDefinedColour = getParameter("userDefinedColour"); widthScale = getParameter("widthScale"); heightScale = getParameter("heightScale"); upperCase = getParameter("upperCase"); file2 = getParameter("file2"); } /** * 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; } public void getLinkParams(Vector links) { String label, url; for (int i = 1; i < 10; i++) { label = getParameter("linkLabel_" + i); url = getParameter("linkURL_" + i); if (label != null && url != null) { links.addElement(label + "|" + url); } } } 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()); } /* * (non-Javadoc) * * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String) */ public String getSelectedSequences(String sep) { return getSelectedSequencesFrom(getDefaultTargetFrame(), sep); } /* * (non-Javadoc) * * @see * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui * .AlignFrame) */ public String getSelectedSequencesFrom(AlignFrame alf) { return getSelectedSequencesFrom(alf, separator); // ""+0x00AC); } /* * (non-Javadoc) * * @see * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui * .AlignFrame, java.lang.String) */ public String getSelectedSequencesFrom(AlignFrame alf, String sep) { StringBuffer result = new StringBuffer(""); if (sep == null || sep.length() == 0) { sep = separator; // "+0x00AC; } if (alf.viewport.getSelectionGroup() != null) { SequenceI[] seqs = alf.viewport.getSelectionGroup() .getSequencesInOrder(alf.viewport.getAlignment()); for (int i = 0; i < seqs.length; i++) { result.append(seqs[i].getName()); result.append(sep); } } return result.toString(); } /* * (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 SequenceIdMatcher matcher = new 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(); SequenceIdMatcher matcher = new 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(getDefaultTargetFrame(), format, suffix); } /* * (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); if (alf.viewport.getSelectionGroup() != null) { // JBPNote: getSelectionAsNewSequence behaviour has changed - this // method now returns a full copy of sequence data // TODO consider using getSequenceSelection instead here String reply = new AppletFormatAdapter().formatSequences(format, new Alignment(alf.viewport.getSelectionAsNewSequence()), seqlimits); return reply; } } catch (Exception ex) { ex.printStackTrace(); return "Error retrieving alignment in " + format + " format. "; } return ""; } /* * (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) { SequenceIdMatcher matcher = new SequenceIdMatcher( alf.viewport.getAlignment().getSequencesArray()); int s = 0; sqs = new SequenceI[ids.length]; for (int i = 0; i < ids.length; i++) { if (ids[i].trim().length() == 0) { continue; } SequenceI sq = matcher.findIdMatch(ids[i]); if (sq != null) { sqs[s++] = sq; } } if (s > 0) { SequenceI[] sqq = new SequenceI[s]; System.arraycopy(sqs, 0, sqq, 0, s); sqs = sqq; } else { sqs = null; } } if (sqs == null) { return ""; } ; final AlignmentOrder aorder = new AlignmentOrder(sqs); if (undoName != null && undoName.trim().length() == 0) { undoName = null; } final String _undoName = undoName; // TODO: deal with synchronization here: cannot raise any events until after // this has returned. return alf.sortBy(aorder, _undoName) ? TRUE : ""; } /* * (non-Javadoc) * * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String) */ public String getAlignment(String format) { return getAlignmentFrom(getDefaultTargetFrame(), format, TRUE); } /* * (non-Javadoc) * * @see * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame, * java.lang.String) */ public String getAlignmentFrom(AlignFrame alf, String format) { return getAlignmentFrom(alf, format, TRUE); } /* * (non-Javadoc) * * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String, * java.lang.String) */ public String getAlignment(String format, String suffix) { return getAlignmentFrom(getDefaultTargetFrame(), format, suffix); } /* * (non-Javadoc) * * @see * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame, * java.lang.String, java.lang.String) */ public String getAlignmentFrom(AlignFrame alf, String format, String suffix) { try { boolean seqlimits = suffix.equalsIgnoreCase(TRUE); String reply = new AppletFormatAdapter().formatSequences(format, alf.viewport.getAlignment(), seqlimits); return reply; } catch (Exception ex) { ex.printStackTrace(); return "Error retrieving alignment in " + format + " format. "; } } /* * (non-Javadoc) * * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String) */ public void loadAnnotation(String annotation) { loadAnnotationFrom(getDefaultTargetFrame(), annotation); } /* * (non-Javadoc) * * @see * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame * , java.lang.String) */ public void loadAnnotationFrom(AlignFrame alf, String annotation) { if (new AnnotationFile().annotateAlignmentView(alf.getAlignViewport(), annotation, AppletFormatAdapter.PASTE)) { alf.alignPanel.fontChanged(); alf.alignPanel.setScrollValues(0, 0); } else { alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE); } } /* * (non-Javadoc) * * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String) */ public void loadFeatures(String features, boolean autoenabledisplay) { loadFeaturesFrom(getDefaultTargetFrame(), features, autoenabledisplay); } /* * (non-Javadoc) * * @see * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame * , java.lang.String) */ public boolean loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay) { return alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE, autoenabledisplay); } /* * (non-Javadoc) * * @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String) */ public String getFeatures(String format) { return getFeaturesFrom(getDefaultTargetFrame(), format); } /* * (non-Javadoc) * * @see * jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame, * java.lang.String) */ public String getFeaturesFrom(AlignFrame alf, String format) { return alf.outputFeatures(false, format); } /* * (non-Javadoc) * * @see jalview.bin.JalviewLiteJsApi#getAnnotation() */ public String getAnnotation() { return getAnnotationFrom(getDefaultTargetFrame()); } /* * (non-Javadoc) * * @see * jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame * ) */ public String getAnnotationFrom(AlignFrame alf) { return alf.outputAnnotations(false); } /* * (non-Javadoc) * * @see jalview.bin.JalviewLiteJsApi#newView() */ public AlignFrame newView() { return newViewFrom(getDefaultTargetFrame()); } /* * (non-Javadoc) * * @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String) */ public AlignFrame newView(String name) { return newViewFrom(getDefaultTargetFrame(), name); } /* * (non-Javadoc) * * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame) */ public AlignFrame newViewFrom(AlignFrame alf) { return alf.newView(null); } /* * (non-Javadoc) * * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame, * java.lang.String) */ public AlignFrame newViewFrom(AlignFrame alf, String name) { return alf.newView(name); } /* * (non-Javadoc) * * @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String, * java.lang.String) */ public AlignFrame loadAlignment(String text, String title) { AlignmentI al = null; String format = new IdentifyFile().Identify(text, AppletFormatAdapter.PASTE); try { al = new AppletFormatAdapter().readFile(text, AppletFormatAdapter.PASTE, format); if (al.getHeight() > 0) { return new AlignFrame(al, this, title, false); } } catch (java.io.IOException ex) { ex.printStackTrace(); } return null; } /* * (non-Javadoc) * * @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String) */ public void setMouseoverListener(String listener) { setMouseoverListener(currentAlignFrame, listener); } private Vector javascriptListeners = new Vector(); /* * (non-Javadoc) * * @see * jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame * , java.lang.String) */ public void setMouseoverListener(AlignFrame af, String listener) { if (listener != null) { listener = listener.trim(); if (listener.length() == 0) { System.err .println("jalview Javascript error: Ignoring empty function for mouseover listener."); return; } } MouseOverListener mol = new 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; } } JsSelectionSender mol = new JsSelectionSender(this, af, listener); javascriptListeners.addElement(mol); StructureSelectionManager.getStructureSelectionManager(this) .addSelectionListener(mol); if (debug) { System.err.println("Added a selection listener for " + ((af == null) ? "All frames" : "Just views for " + af.getAlignViewport().getSequenceSetId())); System.err.println("There are now " + javascriptListeners.size() + " listeners in total."); } } /* * (non-Javadoc) * * @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String, * java.lang.String) */ public void setStructureListener(String listener, String modelSet) { if (listener != null) { listener = listener.trim(); if (listener.length() == 0) { System.err .println("jalview Javascript error: Ignoring empty function for selection listener."); return; } } 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) { 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 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) { EventQueue.invokeLater(new Runnable() { @Override public void run() { try { alf.scrollToColumn(new Integer(leftHandColumn).intValue()); } catch (Exception ex) { System.err .println("Couldn't parse integer arguments (leftHandColumn='" + leftHandColumn + "')"); ex.printStackTrace(); } } }); } // ////////////////////////////////////////////// // ////////////////////////////////////////////// public static int lastFrameX = 200; public static int lastFrameY = 200; boolean fileFound = true; JButton launcher = new JButton( MessageManager.getString("label.start_jalview")); /** * The currentAlignFrame is static, it will change if and when the user * selects a new window. Note that it will *never* point back to the embedded * AlignFrame if the applet is started as embedded on the page and then * afterwards a new view is created. */ public AlignFrame currentAlignFrame = null; /** * This is the first frame to be displayed, and does not change. API calls * will default to this instance if currentAlignFrame is null. */ AlignFrame initialAlignFrame = null; 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; private boolean haveShownLoadMessage; static String builddate = null, version = null, installation = null; private static void initBuildDetails() { if (builddate == null) { builddate = "unknown"; version = "test"; installation = "Webstart"; java.net.URL url = JalviewLite.class .getResource("/.build_properties"); if (url != null) { try { BufferedReader reader = new BufferedReader(new InputStreamReader( url.openStream())); String line; while ((line = reader.readLine()) != null) { if (line.indexOf("VERSION") > -1) { version = line.substring(line.indexOf("=") + 1); } if (line.indexOf("BUILD_DATE") > -1) { builddate = line.substring(line.indexOf("=") + 1); } if (line.indexOf("INSTALLATION") > -1) { installation = line.substring(line.indexOf("=") + 1); } } } catch (Exception ex) { ex.printStackTrace(); } } } } public static String getBuildDate() { initBuildDetails(); return builddate; } public static String getInstallation() { initBuildDetails(); return installation; } public static String getVersion() { initBuildDetails(); return version; } // public JSObject scriptObject = null; /** * init method for Jalview Applet */ public void init() { setParams(); // BH // 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 */ if (debug) { System.err.println("JalviewLite Version " + getVersion()); System.err.println("Build Date : " + getBuildDate()); System.err.println("Installation : " + getInstallation()); } if (externalstructureviewer != null) { useXtrnalSviewer = externalstructureviewer.trim().toLowerCase() .equals(TRUE); } /** * get the separator parameter if present */ if (sep != null) { if (sep.length() > 0) { separator = sep; if (debug) { System.err.println("Separator set to '" + separator + "'"); } } else { throw new Error(MessageManager.getString("error.invalid_separator_parameter")); } } int r = 255; int g = 255; int b = 255; if (rgb != null) { try { r = Integer.parseInt(rgb.substring(0, 2), 16); g = Integer.parseInt(rgb.substring(2, 4), 16); b = Integer.parseInt(rgb.substring(4, 6), 16); } catch (Exception ex) { r = 255; g = 255; b = 255; } } rgb = labelColour; if (rgb != null) { launcher.setLabel(rgb); } setBackground(new Color(r, g, b)); if (startupFile == null) { // Maybe the sequences are added as parameters StringBuffer data = new StringBuffer("PASTE"); int i = 1; while ((startupFile = getParameter("sequence" + i)) != null) { data.append(startupFile.toString() + "\n"); i++; } if (data.length() > 5) { startupFile = data.toString(); } } if (!enableSplitFrame) { file2 = null; } if (embedded) { LoadingThread loader = new LoadingThread(startupFile, file2, this); /** * @j2sNative * * loader.run(); */ { loader.start(); } } else if (startupFile != null) { /* * Start the applet immediately or show a button to start it */ if (!showButton) { LoadingThread loader = new LoadingThread(startupFile, file2, this); loader.start(); } else { add(launcher); launcher.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { LoadingThread loader = new LoadingThread(startupFile, file2, JalviewLite.this); loader.start(); } }); } } else { // jalview initialisation with no alignment. loadAlignment() method can // still be called to open new alignments. startupFile = "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() { 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."); } } } /** * 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 JFrame 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 paintComponent(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); awt2swing.Util.drawString(g, MessageManager.getString("label.jalview_cannot_open_file"), 5, 15); awt2swing.Util.drawString(g, "\"" + startupFile + "\"", 5, 30); } else if (embedded && !haveShownLoadMessage) { g.setColor(Color.black); g.setFont(new Font("Arial", Font.BOLD, 24)); awt2swing.Util.drawString(g, MessageManager.getString("label.jalview_applet"), 50, getSize().height / 2 - 30); awt2swing.Util.drawString(g, MessageManager.getString("label.loading_data") + "...", 50, getSize().height / 2); haveShownLoadMessage = true; } } /** * 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) { 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: protocol for access to file source */ String protocol; String _file; // alignment file or URL spec String _file2; // second alignment file or URL spec JalviewLite applet; private void dbgMsg(String msg) { if (JalviewLite.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, String file2, JalviewLite _applet) { this._file = file; this._file2 = file2; applet = _applet; } public void run() { /** * * @j2sNative * * * System.out.println("BYPASSING JMOL LOADING FOR NOW. THIS WILL BE DONE ANOTHER WAY") * */ { 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."); AlignFrame newAlignFrame = readAlignment(_file); AlignFrame newAlignFrame2 = readAlignment(_file2); if (newAlignFrame != null) { addToDisplay(newAlignFrame, newAlignFrame2); loadTree(newAlignFrame); loadScoreFile(newAlignFrame); loadFeatures(newAlignFrame); loadAnnotations(newAlignFrame); loadJnetFile(newAlignFrame); loadPdbFiles(newAlignFrame); } else { fileFound = false; applet.remove(launcher); applet.repaint(); } callInitCallback(); } /** * Add an AlignFrame to the display; or if two are provided, a SplitFrame. * * @param af * @param af2 */ public void addToDisplay(AlignFrame af, AlignFrame af2) { if (af2 == null) { af.addToDisplay(embedded); } else { SplitFrame sf = new SplitFrame(af, af2); sf.addToDisplay(embedded, JalviewLite.this); } } /** * Read the alignment file (from URL, text 'paste', or archive by * classloader). * * @return */ protected AlignFrame readAlignment(String fileParam) { if (fileParam == null) { return null; } String resolvedFile = setProtocolState(fileParam); String format = new IdentifyFile().Identify(resolvedFile, protocol); dbgMsg("File identified as '" + format + "'"); AlignmentI al = null; try { al = new AppletFormatAdapter().readFile(resolvedFile, protocol, format); if ((al != null) && (al.getHeight() > 0)) { dbgMsg("Successfully loaded file."); al.setDataset(null); AlignFrame newAlignFrame = new AlignFrame(al, applet, resolvedFile, embedded, false); newAlignFrame.setTitle(resolvedFile); if (initialAlignFrame == null) { initialAlignFrame = newAlignFrame; } // update the focus. currentAlignFrame = newAlignFrame; if (protocol == AppletFormatAdapter.PASTE) { newAlignFrame.setTitle(MessageManager.formatMessage( "label.sequences_from", new Object[] { applet.getDocumentBase().toString() })); } newAlignFrame.setStatus(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 { FileParse fp = new FileParse(resolvedFile, protocol); String ln = null; dbgMsg(">>>Dumping contents of '" + resolvedFile + "' " + "(" + 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(); } } } return null; } /** * Load PDBFiles if any specified by parameter(s). Returns true if loaded, * else false. * * @param alignFrame * @return */ protected boolean loadPdbFiles(AlignFrame alignFrame) { boolean result = false; /* * 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 SequenceIdMatcher matcher = (applet.getDefaultParameter( "relaxedidmatch", false)) ? new SequenceIdMatcher( alignFrame.getAlignViewport().getAlignment() .getSequencesArray()) : null; String param; do { if (pdbFileCount > 0) { param = applet.getParameter("PDBFILE" + pdbFileCount); } else { param = 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) { if (sequence != null) { 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(matcher == null ? (Sequence) alignFrame .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); if (seqs != null) { for (int i = 0; i < seqs.length; i++) { if (seqs[i] != null) { ((Sequence) seqs[i]).addPDBId(pdb); StructureSelectionManager.getStructureSelectionManager( applet).registerPDBEntry(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) { 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 = jnetFile; if (param != null) { try { param = setProtocolState(param); AlignFile predictions = GenericFileAdapter.getFile("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 = annotations; if (param != null) { param = setProtocolState(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 = hideFeatureGroups; if (param != null) { alignFrame.setFeatureGroupState(separatorListToArray(param), false); // applet.setFeatureGroupStateOn(newAlignFrame, param, false); } // show specific groups param = showFeatureGroups; if (param != null) { alignFrame.setFeatureGroupState(separatorListToArray(param), true); // applet.setFeatureGroupStateOn(newAlignFrame, param, true); } // and now load features param = features; if (param != null) { param = setProtocolState(param); result = alignFrame.parseFeaturesFile(param, protocol); } param = showFeatureSettings; if (param != null && param.equalsIgnoreCase(TRUE)) { alignFrame.viewport.setShowSequenceFeatures(true); new FeatureSettings(alignFrame.alignPanel); } return result; } /** * Load a score file if specified by parameter. Returns true if file was * loaded, else false. * * @param alignFrame */ protected boolean loadScoreFile(AlignFrame alignFrame) { boolean result = false; if (scoreFile != null && !"".equals(scoreFile)) { try { if (debug) { System.err .println("Attempting to load T-COFFEE score file from the scoreFile parameter"); } result = alignFrame.loadScoreFile(scoreFile); if (!result) { System.err .println("Failed to parse T-COFFEE parameter as a valid score file ('" + scoreFile + "')"); } } catch (Exception e) { System.err.printf("Cannot read score file: '%s'. Cause: %s \n", scoreFile, e.getMessage()); } } return result; } /** * Load a tree for the alignment if specified by parameter. Returns true if * a tree was loaded, else false. * * @param alignFrame * @return */ protected boolean loadTree(AlignFrame alignFrame) { boolean result = false; if (treeFile == null) { treeFile = applet.getParameter("treeFile"); } if (treeFile != null) { try { treeFile = setProtocolState(treeFile); NewickFile fin = new NewickFile(treeFile, protocol); fin.parse(); if (fin.getTree() != null) { alignFrame.loadTree(fin, treeFile); result = true; dbgMsg("Successfully imported tree."); } else { dbgMsg("Tree parameter did not resolve to a valid tree."); } } catch (Exception ex) { ex.printStackTrace(); } } return result; } /** * Discovers whether the given file is in the Applet Archive * * @param file * String * @return boolean */ boolean inArchive(String file) { // This might throw a security exception in certain browsers // Netscape Communicator for instance. try { 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); return false; } } /** * If the file is not already in URL format, tries to locate it by resolving * as a URL. * * @param file * @return */ String addProtocol(final String file) { if (file.indexOf("://") == -1) { /* * Try relative to document base */ String url = applet.resolveUrlForLocalOrAbsolute(file, getDocumentBase()); if (urlExists(url)) { if (debug) { System.err.println("Prepended document base for resource: '" + file + "'"); } return url; } /* * Try relative to codebase */ url = applet.resolveUrlForLocalOrAbsolute(file, getCodeBase()); if (urlExists(url)) { if (debug) { System.err.println("Prepended codebase for resource: '" + file + "'"); } return url; } } /* * Not resolved, leave unchanged */ return file; } /** * Returns true if an input stream can be opened on the specified URL, else * false. * * @param url * @return */ private boolean urlExists(String url) { InputStream is = null; try { is = new URL(url).openStream(); if (is != null) { return true; } } catch (Exception x) { // ignore } finally { if (is != null) { try { is.close(); } catch (IOException e) { // ignore } } } return false; } } /** * @return the default alignFrame acted on by the public applet methods. May * return null with an error message on System.err indicating the * fact. */ public AlignFrame getDefaultTargetFrame() { if (currentAlignFrame != null) { return currentAlignFrame; } if (initialAlignFrame != null) { return initialAlignFrame; } System.err .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use."); return null; } /** * 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 + "'"); } } /* * (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 = ColourSchemeProperty.getAWTColorFromName(colprop); if (col == null) { try { col = new 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() { 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(); // BH removing file name and query int pt = codebase.indexOf("?"); if (pt < 0) pt = codebase.length(); codebase = codebase.substring(0, pt); codebase = codebase.substring(0, codebase.lastIndexOf("/") + 1); // codebase is now http://...xxx/ if (url.indexOf("/") == 0 && !localref.getProtocol().equals("file")) { // http:// https:// we do NOT allow going to the root file system directory! pt = codebase.indexOf("/", 8); return codebase.substring(0, pt) + url; } return codebase + 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; } */ }