X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=75b0add8c24a519380a694c7dc2342b74c2468a0;hb=4f4671d6ef1cb82d03fa9959f4e46d692babc1ef;hp=1801eb1cd38de7a0d5208033e522f8b1a0c41b5c;hpb=af1471fa3d7d3cb32d203e81d394838608dd1c96;p=jalview.git diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java old mode 100755 new mode 100644 index 1801eb1..75b0add --- a/src/jalview/bin/JalviewLite.java +++ b/src/jalview/bin/JalviewLite.java @@ -1,47 +1,69 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * 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. - * + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.bin; +import jalview.analysis.AlignmentUtils; +import jalview.api.AlignFrameI; +import jalview.api.AlignViewportI; +import jalview.api.JalviewApp; +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.HiddenColumns; 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.DataSourceType; +import jalview.io.FileFormatI; +import jalview.io.FileFormats; import jalview.io.FileParse; import jalview.io.IdentifyFile; -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.renderer.seqfeatures.FeatureRenderer; import jalview.structure.SelectionListener; +import jalview.structure.SelectionSource; import jalview.structure.StructureSelectionManager; +import jalview.structure.VamsasSource; +import jalview.util.ColorUtils; +import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; 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; @@ -49,8 +71,12 @@ 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.InputStreamReader; -import java.util.StringTokenizer; +import java.net.URL; +import java.util.ArrayList; +import java.util.Hashtable; +import java.util.List; import java.util.Vector; import netscape.javascript.JSObject; @@ -59,67 +85,91 @@ import netscape.javascript.JSObject; * Jalview Applet. Runs in Java 1.18 runtime * * @author $author$ - * @version $Revision$ + * @version $Revision: 1.92 $ */ +@SuppressWarnings("serial") public class JalviewLite extends Applet + implements StructureSelectionManagerProvider, JalviewLiteJsApi, + JalviewApp { + public JalviewLite() + { + appLoader = new JalviewAppLoader(debug); + } + private static final String TRUE = "true"; + + private static final String FALSE = "false"; + + public StructureSelectionManager getStructureSelectionManager() + { + return StructureSelectionManager.getStructureSelectionManager(this); + } + + @Override + public StructureSelectionManagerProvider getStructureSelectionManagerProvider() + { + return 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 the - * 'boolean not' character (""+0x00AC) or (¬) + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences() */ + @Override public String getSelectedSequences() { return getSelectedSequencesFrom(getDefaultTargetFrame()); } - /** - * @param sep - * separator string or null for default - * @return String list of selected sequence IDs, each terminated by given - * separator string + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String) */ + @Override public String getSelectedSequences(String sep) { return getSelectedSequencesFrom(getDefaultTargetFrame(), sep); } - /** - * @param alf - * alignframe containing selection - * @return String list of selected sequence IDs, each terminated by current - * default separator sequence + /* + * (non-Javadoc) * + * @see + * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui + * .AlignFrame) */ - public String getSelectedSequencesFrom(AlignFrame alf) + @Override + public String getSelectedSequencesFrom(AlignFrameI 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 'boolean not' - * @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) + @Override + public String getSelectedSequencesFrom(AlignFrameI alf, String sep) { StringBuffer result = new StringBuffer(""); if (sep == null || sep.length() == 0) { sep = separator; // "+0x00AC; } - if (alf.viewport.getSelectionGroup() != null) + if (((AlignFrame) alf).viewport.getSelectionGroup() != null) { - SequenceI[] seqs = alf.viewport.getSelectionGroup() - .getSequencesInOrder(alf.viewport.getAlignment()); + SequenceI[] seqs = ((AlignFrame) alf).viewport.getSelectionGroup() + .getSequencesInOrder( + ((AlignFrame) alf).viewport.getAlignment()); for (int i = 0; i < seqs.length; i++) { @@ -131,16 +181,13 @@ public class JalviewLite extends Applet return result.toString(); } - /** + /* + * (non-Javadoc) * - * @param sequenceId - * id of sequence to highlight - * @param position - * integer position [ tobe implemented or range ] on sequence - * @param alignedPosition - * true/false/empty string - indicate if position is an alignment - * column or unaligned sequence position + * @see jalview.bin.JalviewLiteJsApi#highlight(java.lang.String, + * java.lang.String, java.lang.String) */ + @Override public void highlight(String sequenceId, String position, String alignedPosition) { @@ -148,26 +195,23 @@ public class JalviewLite extends Applet alignedPosition); } - /** + /* + * (non-Javadoc) * - * @param sequenceId - * id of sequence to highlight - * @param position - * integer position [ tobe implemented or range ] on sequence - * @param alignedPosition - * false, blank or something else - indicate if position is an - * alignment column or unaligned sequence position + * @see jalview.bin.JalviewLiteJsApi#highlightIn(jalview.appletgui.AlignFrame, + * java.lang.String, java.lang.String, java.lang.String) */ - public void highlightIn(AlignFrame alf, String sequenceId, - String position, String alignedPosition) + @Override + public void highlightIn(final AlignFrameI 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()); - SequenceI sq = matcher.findIdMatch(sequenceId); + ((AlignFrame) alf).viewport.getAlignment().getSequencesArray()); + final SequenceI sq = matcher.findIdMatch(sequenceId); if (sq != null) { - int pos, apos = -1; + int apos = -1; try { apos = new Integer(position).intValue(); @@ -176,75 +220,82 @@ public class JalviewLite extends Applet { return; } + final StructureSelectionManagerProvider me = this; + final int pos = apos; // use vamsas listener to broadcast to all listeners in scope - if (alignedPosition != null - && (alignedPosition.trim().length() == 0 || alignedPosition - .toLowerCase().indexOf("false") > -1)) + if (alignedPosition != null && (alignedPosition.trim().length() == 0 + || alignedPosition.toLowerCase().indexOf("false") > -1)) { - StructureSelectionManager.getStructureSelectionManager() - .mouseOverVamsasSequence(sq, sq.findIndex(apos), null); + java.awt.EventQueue.invokeLater(new Runnable() + { + @Override + public void run() + { + StructureSelectionManager.getStructureSelectionManager(me) + .mouseOverVamsasSequence(sq, sq.findIndex(pos), null); + } + }); } else { - StructureSelectionManager.getStructureSelectionManager() - .mouseOverVamsasSequence(sq, apos, null); + java.awt.EventQueue.invokeLater(new Runnable() + { + @Override + public void run() + { + StructureSelectionManager.getStructureSelectionManager(me) + .mouseOverVamsasSequence(sq, pos, null); + } + }); } - } } - /** - * select regions of the currrent alignment frame + /* + * (non-Javadoc) * - * @param sequenceIds - * String separated list of sequence ids or empty string - * @param columns - * String separated list { column range or column, ..} or empty - * string + * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String, + * java.lang.String) */ + @Override public void select(String sequenceIds, String columns) { selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator); } - /** - * select regions of the currrent alignment frame + /* + * (non-Javadoc) * - * @param toselect - * String separated list { column range, seq1...seqn sequence ids } - * @param sep - * separator between toselect fields + * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String, + * java.lang.String, java.lang.String) */ + @Override public void select(String sequenceIds, String columns, String sep) { selectIn(getDefaultTargetFrame(), sequenceIds, columns, sep); } - /** - * select regions of the given alignment frame + /* + * (non-Javadoc) * - * @param alf - * @param toselect - * String separated list { column range, seq1...seqn sequence ids } - * @param sep - * separator between toselect fields + * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame, + * java.lang.String, java.lang.String) */ - public void selectIn(AlignFrame alf, String sequenceIds, String columns) + @Override + public void selectIn(AlignFrameI alf, String sequenceIds, String columns) { selectIn(alf, sequenceIds, columns, separator); } - /** - * select regions of the given alignment frame + /* + * (non-Javadoc) * - * @param alf - * @param toselect - * String separated list { column range, seq1...seqn sequence ids } - * @param sep - * separator between toselect fields + * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame, + * java.lang.String, java.lang.String, java.lang.String) */ - public void selectIn(AlignFrame alf, String sequenceIds, String columns, - String sep) + @Override + public void selectIn(final AlignFrameI alf, String sequenceIds, + String columns, String sep) { if (sep == null || sep.length() == 0) { @@ -259,13 +310,13 @@ public class JalviewLite extends Applet } } // deparse fields - String[] ids = separatorListToArray(sequenceIds, sep); - String[] cols = separatorListToArray(columns, sep); - SequenceGroup sel = new SequenceGroup(); - ColumnSelection csel = new ColumnSelection(); - AlignmentI al = alf.viewport.getAlignment(); + String[] ids = JalviewAppLoader.separatorListToArray(sequenceIds, sep); + String[] cols = JalviewAppLoader.separatorListToArray(columns, sep); + final SequenceGroup sel = new SequenceGroup(); + final ColumnSelection csel = new ColumnSelection(); + AlignmentI al = ((AlignFrame) alf).viewport.getAlignment(); jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher( - alf.viewport.getAlignment().getSequencesArray()); + ((AlignFrame) alf).viewport.getAlignment().getSequencesArray()); int start = 0, end = al.getWidth(), alw = al.getWidth(); boolean seqsfound = true; if (ids != null && ids.length > 0) @@ -306,8 +357,8 @@ public class JalviewLite extends Applet from--; } catch (NumberFormatException ex) { - System.err - .println("ERROR: Couldn't parse first integer in range element column selection string '" + System.err.println( + "ERROR: Couldn't parse first integer in range element column selection string '" + cl + "' - format is 'from-to'"); return; } @@ -317,8 +368,8 @@ public class JalviewLite extends Applet to--; } catch (NumberFormatException ex) { - System.err - .println("ERROR: Couldn't parse second integer in range element column selection string '" + System.err.println( + "ERROR: Couldn't parse second integer in range element column selection string '" + cl + "' - format is 'from-to'"); return; } @@ -384,8 +435,8 @@ public class JalviewLite extends Applet } else { - System.err - .println("ERROR: Couldn't parse integer from point selection element of column selection string '" + System.err.println( + "ERROR: Couldn't parse integer from point selection element of column selection string '" + cl + "'"); return; } @@ -435,89 +486,113 @@ public class JalviewLite extends Applet SequenceI rs = sel.getSequenceAt(0); start = rs.findIndex(start); end = rs.findIndex(end); - if (csel != null) + List cs = new ArrayList<>(csel.getSelected()); + csel.clear(); + for (Integer selectedCol : cs) { - Vector cs = csel.getSelected(); - csel.clear(); - for (int csi = 0, csiS = cs.size(); csi < csiS; csi++) - { - csel.addElement(rs.findIndex(((Integer) cs.elementAt(csi)) - .intValue())); - } + csel.addElement(rs.findIndex(selectedCol)); } } sel.setStartRes(start); sel.setEndRes(end); - alf.select(sel, csel); + EventQueue.invokeLater(new Runnable() + { + @Override + public void run() + { + ((AlignFrame) alf).select(sel, csel, ((AlignFrame) alf) + .getAlignViewport().getAlignment().getHiddenColumns()); + } + }); } } - /** - * get sequences selected in current alignFrame and return their alignment in - * format 'format' either with or without suffix + /* + * (non-Javadoc) * - * @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 + * @see + * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignment(java.lang. + * String, java.lang.String) */ - public String getSelectedSequencesAsAlignment(String format, String suffix) + @Override + public String getSelectedSequencesAsAlignment(String format, + String suffix) { return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(), format, suffix); } - /** - * get sequences selected in alf and return their alignment in format 'format' - * either with or without suffix + /* + * (non-Javadoc) * - * @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 - */ - public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, + * @see + * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignmentFrom(jalview + * .appletgui.AlignFrame, java.lang.String, java.lang.String) + */ + @Override + public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf, String format, String suffix) { try { - boolean seqlimits = suffix.equalsIgnoreCase("true"); - if (alf.viewport.getSelectionGroup() != null) + FileFormatI theFormat = FileFormats.getInstance().forName(format); + boolean seqlimits = suffix.equalsIgnoreCase(TRUE); + if (((AlignFrame) alf).viewport.getSelectionGroup() != null) { - String reply = new AppletFormatAdapter().formatSequences(format, - new Alignment(alf.viewport.getSelectionAsNewSequence()), + // 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(theFormat, + new Alignment(((AlignFrame) alf).viewport + .getSelectionAsNewSequence()), seqlimits); return reply; } - } catch (Exception ex) + } catch (IllegalArgumentException ex) { ex.printStackTrace(); - return "Error retrieving alignment in " + format + " format. "; + return "Error retrieving alignment, possibly invalid format specifier: " + + format; } return ""; } + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder() + */ + @Override public String getAlignmentOrder() { return getAlignmentOrderFrom(getDefaultTargetFrame()); } - public String getAlignmentOrderFrom(AlignFrame alf) + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame + * ) + */ + @Override + public String getAlignmentOrderFrom(AlignFrameI alf) { return getAlignmentOrderFrom(alf, separator); } - public String getAlignmentOrderFrom(AlignFrame alf, String sep) + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame + * , java.lang.String) + */ + @Override + public String getAlignmentOrderFrom(AlignFrameI alf, String sep) { - AlignmentI alorder = alf.getAlignViewport().getAlignment(); + AlignmentI alorder = ((AlignFrame) alf).getAlignViewport() + .getAlignment(); String[] order = new String[alorder.getHeight()]; for (int i = 0; i < order.length; i++) { @@ -526,25 +601,48 @@ public class JalviewLite extends Applet return arrayToSeparatorList(order); } + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String, + * java.lang.String) + */ + @Override 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) + */ + @Override public String orderBy(String order, String undoName, String sep) { return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep); } - public String orderAlignmentBy(AlignFrame alf, String order, + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#orderAlignmentBy(jalview.appletgui.AlignFrame, + * java.lang.String, java.lang.String, java.lang.String) + */ + @Override + public String orderAlignmentBy(AlignFrameI alf, String order, String undoName, String sep) { - String[] ids = separatorListToArray(order, sep); + String[] ids = JalviewAppLoader.separatorListToArray(order, sep); SequenceI[] sqs = null; if (ids != null && ids.length > 0) { jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher( - alf.viewport.getAlignment().getSequencesArray()); + ((AlignFrame) alf).viewport.getAlignment() + .getSequencesArray()); int s = 0; sqs = new SequenceI[ids.length]; for (int i = 0; i < ids.length; i++) @@ -575,235 +673,409 @@ public class JalviewLite extends Applet return ""; } ; - AlignmentOrder aorder = new AlignmentOrder(sqs); + final AlignmentOrder aorder = new AlignmentOrder(sqs); if (undoName != null && undoName.trim().length() == 0) { undoName = null; } - - return alf.sortBy(aorder, undoName) ? "true" : ""; + final String _undoName = undoName; + // TODO: deal with synchronization here: cannot raise any events until after + // this has returned. + return ((AlignFrame) alf).sortBy(aorder, _undoName) ? TRUE : ""; } + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String) + */ + @Override public String getAlignment(String format) { - return getAlignmentFrom(getDefaultTargetFrame(), format, "true"); + return getAlignmentFrom(getDefaultTargetFrame(), format, TRUE); } - public String getAlignmentFrom(AlignFrame alf, String format) + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame, + * java.lang.String) + */ + @Override + public String getAlignmentFrom(AlignFrameI 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) + */ + @Override public String getAlignment(String format, String suffix) { return getAlignmentFrom(getDefaultTargetFrame(), format, suffix); } - public String getAlignmentFrom(AlignFrame alf, String format, + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame, + * java.lang.String, java.lang.String) + */ + @Override + public String getAlignmentFrom(AlignFrameI 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); + FileFormatI theFormat = FileFormats.getInstance().forName(format); + String reply = new AppletFormatAdapter().formatSequences(theFormat, + ((AlignFrame) alf).viewport.getAlignment(), seqlimits); return reply; - } catch (Exception ex) + } catch (IllegalArgumentException ex) { ex.printStackTrace(); - return "Error retrieving alignment in " + format + " format. "; + return "Error retrieving alignment, possibly invalid format specifier: " + + format; } } + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String) + */ + @Override public void loadAnnotation(String annotation) { loadAnnotationFrom(getDefaultTargetFrame(), annotation); } - public void loadAnnotationFrom(AlignFrame alf, String annotation) + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame + * , java.lang.String) + */ + @Override + public void loadAnnotationFrom(AlignFrameI alf, String annotation) { - if (new AnnotationFile().readAnnotationFile(alf.getAlignViewport() - .getAlignment(), annotation, AppletFormatAdapter.PASTE)) + if (new AnnotationFile().annotateAlignmentView( + ((AlignFrame) alf).getAlignViewport(), + annotation, DataSourceType.PASTE)) { - alf.alignPanel.fontChanged(); - alf.alignPanel.setScrollValues(0, 0); + ((AlignFrame) alf).alignPanel.fontChanged(); + ((AlignFrame) alf).alignPanel.setScrollValues(0, 0); } else { - alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE); + ((AlignFrame) alf).parseFeaturesFile(annotation, + DataSourceType.PASTE); } } + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String) + */ + @Override + public void loadFeatures(String features, boolean autoenabledisplay) + { + loadFeaturesFrom(getDefaultTargetFrame(), features, autoenabledisplay); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame + * , java.lang.String) + */ + @Override + public boolean loadFeaturesFrom(AlignFrameI alf, String features, + boolean autoenabledisplay) + { + return ((AlignFrame) alf).parseFeaturesFile(features, + DataSourceType.PASTE, + autoenabledisplay); + } + + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String) + */ + @Override public String getFeatures(String format) { return getFeaturesFrom(getDefaultTargetFrame(), format); } - public String getFeaturesFrom(AlignFrame alf, String format) + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame, + * java.lang.String) + */ + @Override + public String getFeaturesFrom(AlignFrameI alf, String format) { - return alf.outputFeatures(false, format); + return ((AlignFrame) alf).outputFeatures(false, format); } + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#getAnnotation() + */ + @Override public String getAnnotation() { return getAnnotationFrom(getDefaultTargetFrame()); } - public String getAnnotationFrom(AlignFrame alf) + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame + * ) + */ + @Override + public String getAnnotationFrom(AlignFrameI alf) { - return alf.outputAnnotations(false); + return ((AlignFrame) alf).outputAnnotations(false); } + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#newView() + */ + @Override public AlignFrame newView() { return newViewFrom(getDefaultTargetFrame()); } + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String) + */ + @Override public AlignFrame newView(String name) { return newViewFrom(getDefaultTargetFrame(), name); } - public AlignFrame newViewFrom(AlignFrame alf) + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame) + */ + @Override + public AlignFrame newViewFrom(AlignFrameI alf) { - return alf.newView(null); + return ((AlignFrame) alf).newView(null); } - public AlignFrame newViewFrom(AlignFrame alf, String name) + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame, + * java.lang.String) + */ + @Override + public AlignFrame newViewFrom(AlignFrameI alf, String name) { - return alf.newView(name); + return ((AlignFrame) 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) */ + @Override public AlignFrame loadAlignment(String text, String title) { - Alignment al = null; + AlignmentI al = null; - String format = new IdentifyFile().Identify(text, - AppletFormatAdapter.PASTE); try { - al = new AppletFormatAdapter().readFile(text, - AppletFormatAdapter.PASTE, format); + FileFormatI format = new IdentifyFile().identify(text, + DataSourceType.PASTE); + al = new AppletFormatAdapter().readFile(text, DataSourceType.PASTE, + format); if (al.getHeight() > 0) { return new AlignFrame(al, this, title, false); } - } catch (java.io.IOException ex) + } catch (IOException ex) { ex.printStackTrace(); } return null; } + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String) + */ + @Override public void setMouseoverListener(String listener) { setMouseoverListener(currentAlignFrame, listener); } - private Vector javascriptListeners = new Vector(); + private Vector javascriptListeners = new Vector<>(); - public void setMouseoverListener(AlignFrame af, String listener) + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame + * , java.lang.String) + */ + @Override + public void setMouseoverListener(AlignFrameI 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."); + System.err.println( + "jalview Javascript error: Ignoring empty function for mouseover listener."); return; } } jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener( - this, af, listener); + this, (AlignFrame) af, listener, debug); javascriptListeners.addElement(mol); - StructureSelectionManager.getStructureSelectionManager() + 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())); + + ((af == null) ? "All frames" + : "Just views for " + + ((AlignFrame) af).getAlignViewport() + .getSequenceSetId())); System.err.println("There are now " + javascriptListeners.size() + " listeners in total."); } } + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String) + */ + @Override public void setSelectionListener(String listener) { setSelectionListener(null, listener); } - public void setSelectionListener(AlignFrame af, String listener) + /* + * (non-Javadoc) + * + * @see + * jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame + * , java.lang.String) + */ + @Override + public void setSelectionListener(AlignFrameI 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."); + System.err.println( + "jalview Javascript error: Ignoring empty function for selection listener."); return; } } jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender( - this, af, listener); + this, (AlignFrame) af, listener, debug); javascriptListeners.addElement(mol); - StructureSelectionManager.getStructureSelectionManager() + 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())); + + ((af == null) ? "All frames" + : "Just views for " + + ((AlignFrame) af).getAlignViewport() + .getSequenceSetId())); System.err.println("There are now " + javascriptListeners.size() + " listeners in total."); } } - public void setStructureListener(String listener) + /** + * 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) + */ + @Override + 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."); + System.err.println( + "jalview Javascript error: Ignoring empty function for selection listener."); return; } } - jalview.javascript.MouseOverStructureListener mol = new jalview.javascript.MouseOverStructureListener(this, listener); + MouseOverStructureListener mol = new MouseOverStructureListener(this, + listener, separatorListToArray(modelSet), debug); javascriptListeners.addElement(mol); - StructureSelectionManager.getStructureSelectionManager() + StructureSelectionManager.getStructureSelectionManager(this) .addStructureViewerListener(mol); if (debug) { - System.err.println("Added a javascript structure viewer listener '"+listener+"'"); + System.err.println("Added a javascript structure viewer listener '" + + listener + "'"); System.err.println("There are now " + javascriptListeners.size() + " listeners in total."); } } - /** - * remove any callback using the given listener function and associated with - * the given alignFrame (or null for all callbacks) + + /* + * (non-Javadoc) * - * @param af - * (may be null) - * @param listener - * (may be null) + * @see + * jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui + * .AlignFrame, java.lang.String) */ - public void removeJavascriptListener(AlignFrame af, String listener) + @Override + public void removeJavascriptListener(AlignFrameI af, String listener) { if (listener != null) { @@ -818,20 +1090,19 @@ public class JalviewLite extends Applet { Object lstn = javascriptListeners.elementAt(ms); JsCallBack lstner = (JsCallBack) lstn; - if ((af == null || lstner.getAlignFrame() == af) - && (listener == null || lstner.getListenerFunction().equals( - listener))) + if ((af == null || lstner.getAlignFrame() == af) && (listener == null + || lstner.getListenerFunction().equals(listener))) { javascriptListeners.removeElement(lstner); msSize--; if (lstner instanceof SelectionListener) { - StructureSelectionManager.getStructureSelectionManager() + StructureSelectionManager.getStructureSelectionManager(this) .removeSelectionListener((SelectionListener) lstner); } else { - StructureSelectionManager.getStructureSelectionManager() + StructureSelectionManager.getStructureSelectionManager(this) .removeStructureViewerListener(lstner, null); } rprt = debug; @@ -852,50 +1123,195 @@ public class JalviewLite extends Applet } } + @Override public void stop() { + System.err.println("Applet " + getName() + " stop()."); + tidyUp(); + } + + @Override + 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) { - Object mol = javascriptListeners.elementAt(0); + jalview.javascript.JSFunctionExec mol = javascriptListeners + .elementAt(0); javascriptListeners.removeElement(mol); if (mol instanceof SelectionListener) { - StructureSelectionManager.getStructureSelectionManager() + StructureSelectionManager.getStructureSelectionManager(this) .removeSelectionListener((SelectionListener) mol); } else { - StructureSelectionManager.getStructureSelectionManager() + StructureSelectionManager.getStructureSelectionManager(this) .removeStructureViewerListener(mol, null); } + mol.jvlite = null; } } - jalview.javascript.JSFunctionExec.stopQueue(); + if (jsFunctionExec != null) + { + jsFunctionExec.tidyUp(); + jsFunctionExec = null; + } + initialAlignFrame = null; + javascriptListeners = null; + StructureSelectionManager.release(this); } - /** - * send a mouseover message to all the alignment windows associated with the - * given residue in the pdbfile + private jalview.javascript.JSFunctionExec jsFunctionExec; + + /* + * (non-Javadoc) * - * @param pdbResNum - * @param chain - * @param pdbfile + * @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String, + * java.lang.String, java.lang.String) */ - public void mouseOverStructure(String pdbResNum, String chain, String pdbfile) + @Override + public void mouseOverStructure(final String pdbResNum, final String chain, + final String pdbfile) { - try { - StructureSelectionManager.getStructureSelectionManager() - .mouseOverStructure(new Integer(pdbResNum).intValue(), chain, pdbfile); - if (debug) + final StructureSelectionManagerProvider me = this; + java.awt.EventQueue.invokeLater(new Runnable() { - System.err.println("mouseOver for '"+pdbResNum+"' in chain '"+chain+"' in structure '"+pdbfile+"'"); - } - } catch (NumberFormatException e) + @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) + */ + @Override + public void scrollViewToIn(final AlignFrameI alf, final String topRow, + final String leftHandColumn) + { + java.awt.EventQueue.invokeLater(new Runnable() { - System.err.println("Ignoring invalid residue number string '"+pdbResNum+"'"); - } + @Override + public void run() + { + try + { + ((AlignFrame) 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 AlignFrameI alf, final String topRow) + { + + java.awt.EventQueue.invokeLater(new Runnable() + { + @Override + public void run() + { + try + { + ((AlignFrame) 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 AlignFrameI alf, + final String leftHandColumn) + { + java.awt.EventQueue.invokeLater(new Runnable() + { + + @Override + public void run() + { + try + { + ((AlignFrame) alf) + .scrollToColumn(new Integer(leftHandColumn).intValue()); + + } catch (Exception ex) + { + System.err.println( + "Couldn't parse integer arguments (leftHandColumn='" + + leftHandColumn + "')"); + ex.printStackTrace(); + } + } + }); + } // ////////////////////////////////////////////// @@ -909,7 +1325,10 @@ public class JalviewLite extends Applet 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 @@ -927,9 +1346,9 @@ public class JalviewLite extends Applet boolean embedded = false; - private boolean checkForJmol = true; + boolean checkForJmol = true; - private boolean checkedForJmol = false; // ensure we don't check for jmol + boolean checkedForJmol = false; // ensure we don't check for jmol // every time the app is re-inited @@ -938,13 +1357,18 @@ public class JalviewLite extends Applet private boolean alignPdbStructures = false; /** - * use an external structure viewer exclusively (no jmols or MCViews will be opened by JalviewLite itself) + * use an external structure viewer exclusively (no jmols or mc_views will be + * opened by JalviewLite itself) */ - public boolean useXtrnalSviewer=false; + public boolean useXtrnalSviewer = false; + + public JalviewAppLoader appLoader; + + public AlignFrame loaderFrame; public static boolean debug = false; - static String builddate = null, version = null; + static String builddate = null, version = null, installation = null; private static void initBuildDetails() { @@ -952,14 +1376,15 @@ public class JalviewLite extends Applet { 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())); + BufferedReader reader = new BufferedReader( + new InputStreamReader(url.openStream())); String line; while ((line = reader.readLine()) != null) { @@ -971,6 +1396,10 @@ public class JalviewLite extends Applet { builddate = line.substring(line.indexOf("=") + 1); } + if (line.indexOf("INSTALLATION") > -1) + { + installation = line.substring(line.indexOf("=") + 1); + } } } catch (Exception ex) { @@ -986,6 +1415,12 @@ public class JalviewLite extends Applet return builddate; } + public static String getInstallation() + { + initBuildDetails(); + return installation; + } + public static String getVersion() { initBuildDetails(); @@ -997,9 +1432,10 @@ public class JalviewLite extends Applet /** * init method for Jalview Applet */ + @Override public void init() { - // remove any handlers that might be hanging around from an earlier instance + debug = TRUE.equalsIgnoreCase(getParameter("debug")); try { if (debug) @@ -1015,32 +1451,24 @@ public class JalviewLite extends Applet } catch (Exception ex) { - System.err - .println("Warning: No JalviewLite javascript callbacks available."); + System.err.println( + "Warning: No JalviewLite javascript callbacks available."); if (debug) { ex.printStackTrace(); } } - /** - * turn on extra applet debugging - */ - String dbg = getParameter("debug"); - if (dbg != null) - { - debug = dbg.toLowerCase().equals("true"); - } + if (debug) { - System.err.println("JalviewLite Version " + getVersion()); System.err.println("Build Date : " + getBuildDate()); - + System.err.println("Installation : " + getInstallation()); } String externalsviewer = getParameter("externalstructureviewer"); - if (externalsviewer!=null) + if (externalsviewer != null) { - useXtrnalSviewer=externalsviewer.trim().toLowerCase().equals("true"); + useXtrnalSviewer = externalsviewer.trim().toLowerCase().equals(TRUE); } /** * if true disable the check for jmol @@ -1048,7 +1476,7 @@ public class JalviewLite extends Applet String chkforJmol = getParameter("nojmol"); if (chkforJmol != null) { - checkForJmol = !chkforJmol.equals("true"); + checkForJmol = !chkforJmol.equals(TRUE); } /** * get the separator parameter if present @@ -1066,10 +1494,13 @@ public class JalviewLite extends Applet } else { - throw new Error( - "Invalid separator parameter - must be non-zero length"); + throw new Error(MessageManager + .getString("error.invalid_separator_parameter")); } } + + // Background color + int r = 255; int g = 255; int b = 255; @@ -1089,100 +1520,126 @@ public class JalviewLite extends Applet b = 255; } } + setBackground(new Color(r, g, b)); + param = getParameter("label"); if (param != null) { launcher.setLabel(param); } - setBackground(new Color(r, g, b)); - file = getParameter("file"); if (file == null) { - // Maybe the sequences are added as parameters - StringBuffer data = new StringBuffer("PASTE"); - int i = 1; - while ((file = getParameter("sequence" + i)) != null) - { - data.append(file.toString() + "\n"); - i++; - } - if (data.length() > 5) - { - file = data.toString(); - } + file = appLoader.getPastedSequence(this); } - - final JalviewLite jvapplet = this; - if (getParameter("embedded") != null - && getParameter("embedded").equalsIgnoreCase("true")) + if (getDefaultParameter("enableSplitFrame", true)) { - // Launch as embedded applet in page - embedded = true; - LoadingThread loader = new LoadingThread(file, jvapplet); - loader.start(); + file2 = getParameter("file2"); } - else if (file != null) + + embedded = (TRUE.equalsIgnoreCase(getParameter("embedded")) + || file != null + && FALSE.equalsIgnoreCase(getParameter("showbutton"))); + if (embedded) { - if (getParameter("showbutton") == null - || !getParameter("showbutton").equalsIgnoreCase("false")) - { - // Add the JalviewLite 'Button' to the page - add(launcher); - launcher.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - LoadingThread loader = new LoadingThread(file, jvapplet); - loader.start(); - } - }); - } - else - { - // Open jalviewLite immediately. - LoadingThread loader = new LoadingThread(file, jvapplet); - loader.start(); - } + startLoading(); } - else + else if (file == null) { // jalview initialisation with no alignment. loadAlignment() method can // still be called to open new alignments. file = "NO FILE"; fileFound = false; - // callInitCallback(); + callInitCallback(); + } + else + { + add(launcher); + launcher.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + startLoading(); + } + }); } } - private void callInitCallback() + protected void startLoading() { - String initjscallback = getParameter("oninit"); - if (initjscallback == null) - { - return; - } - initjscallback = initjscallback.trim(); - if (initjscallback.length() > 0) + LoadingThread loader = new LoadingThread(file, file2, this); + loader.start(); + } + + private void initLiveConnect() + { + // try really hard to get the liveConnect thing working + boolean notFailed = false; + int tries = 0; + while (!notFailed && tries < 10) { - JSObject scriptObject = null; + if (tries > 0) + { + System.err.println("LiveConnect request thread going to sleep."); + } try { - scriptObject = JSObject.getWindow(this); - } catch (Exception ex) + Thread.sleep(700 * (1 + tries)); + } catch (InterruptedException q) { } ; - if (scriptObject != null) + if (tries++ > 0) { - try + System.err.println("LiveConnect request thread woken up."); + } + try + { + JSObject scriptObject = JSObject.getWindow(this); + if (scriptObject.eval("navigator") != null) { - // do onInit with the JS executor thread - new JSFunctionExec(this).executeJavascriptFunction(true, - initjscallback, null, "Calling oninit callback '" - + initjscallback + "'."); + notFailed = true; + } + } catch (Exception jsex) + { + System.err.println("Attempt " + tries + + " to access LiveConnect javascript failed."); + } + } + } + + 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, debug).executeJavascriptFunction(true, + initjscallback, null, + "Calling oninit callback '" + initjscallback + "'."); } catch (Exception e) { System.err.println("Exception when executing _oninit callback '" @@ -1220,15 +1677,20 @@ public class JalviewLite extends Applet frame.setTitle(title); frame.addWindowListener(new WindowAdapter() { + @Override public void windowClosing(WindowEvent e) { if (frame instanceof AlignFrame) { + AlignViewport vp = ((AlignFrame) frame).viewport; ((AlignFrame) frame).closeMenuItem_actionPerformed(); - if (((AlignFrame) frame).viewport.applet.currentAlignFrame == frame) + if (vp.applet.currentAlignFrame == frame) { - ((AlignFrame) frame).viewport.applet.currentAlignFrame = null; + vp.applet.currentAlignFrame = null; } + vp.applet = null; + vp = null; + } lastFrameX -= 40; lastFrameY -= 40; @@ -1240,6 +1702,7 @@ public class JalviewLite extends Applet frame.dispose(); } + @Override public void windowActivated(WindowEvent e) { if (frame instanceof AlignFrame) @@ -1277,6 +1740,7 @@ public class JalviewLite extends Applet * @param g * graphics context */ + @Override public void paint(Graphics g) { if (!fileFound) @@ -1285,15 +1749,19 @@ 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, getSize().height / 2 - 30); - g.drawString("Loading Data...", 50, 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); } } @@ -1324,6 +1792,7 @@ public class JalviewLite extends Applet { private boolean running = false; + @Override public void run() { if (running || checkedForJmol) @@ -1342,8 +1811,8 @@ public class JalviewLite extends Applet } if (!jmolAvailable) { - System.out - .println("Jmol not available - Using MCview for structures"); + System.out.println( + "Jmol not available - Using mc_view for structures"); } } catch (java.lang.ClassNotFoundException ex) { @@ -1354,8 +1823,8 @@ public class JalviewLite extends Applet jmolAvailable = false; if (debug) { - System.err - .println("Skipping Jmol check. Will use MCView (probably)"); + System.err.println( + "Skipping Jmol check. Will use mc_view (probably)"); } } checkedForJmol = true; @@ -1371,27 +1840,19 @@ public class JalviewLite extends Applet class LoadingThread extends Thread { /** - * State variable: File source - */ - String file; - - /** * State variable: protocol for access to file source */ - String protocol; + DataSourceType protocol; - /** - * State variable: format of file source - */ - String format; + String _file; // alignment file or URL spec - String _file; + String _file2; // second alignment file or URL spec JalviewLite applet; - private void dbgMsg(String msg) + public void dbgMsg(String msg) { - if (applet.debug) + if (JalviewLite.debug) { System.err.println(msg); } @@ -1401,35 +1862,25 @@ 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")) - { - 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; + + String[] ret = new String[] { path }; + protocol = JalviewAppLoader.resolveFileProtocol(applet, ret); + return ret[0]; } - public LoadingThread(String _file, JalviewLite _applet) + public LoadingThread(String file, String file2, JalviewLite _applet) { - this._file = _file; + this._file = file; + this._file2 = file2; applet = _applet; } + @Override public void run() { LoadJmolThread jmolchecker = new LoadJmolThread(); @@ -1443,378 +1894,149 @@ public class JalviewLite extends Applet } catch (Exception e) { } - ; } startLoading(); // applet.callInitCallback(); } + /** + * Load the alignment and any related files as specified by applet + * parameters + */ private void startLoading() { - AlignFrame newAlignFrame; - dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile"); - file = setProtocolState(_file); + dbgMsg("Loading thread started with:\n>>file\n" + _file + + ">>endfile"); - format = new jalview.io.IdentifyFile().Identify(file, protocol); - dbgMsg("File identified as '" + format + "'"); dbgMsg("Loading started."); - Alignment al = null; - try + + AlignFrame newAlignFrame = readAlignment(_file); + AlignFrame newAlignFrame2 = readAlignment(_file2); + if (newAlignFrame != null) { - al = new AppletFormatAdapter().readFile(file, protocol, format); - } catch (java.io.IOException ex) + addToDisplay(newAlignFrame, newAlignFrame2); + applet.loaderFrame = newAlignFrame; + appLoader.load(applet); + } + else { - dbgMsg("File load exception."); - ex.printStackTrace(); - if (debug) - { - try - { - FileParse fp = new FileParse(file, protocol); - String ln = null; - dbgMsg(">>>Dumping contents of '" + file + "' " + "(" - + protocol + ")"); - while ((ln = fp.nextLine()) != null) - { - dbgMsg(ln); - } - dbgMsg(">>>Dump finished."); - } catch (Exception e) - { - System.err - .println("Exception when trying to dump the content of the file parameter."); - e.printStackTrace(); - } - } + fileFound = false; + applet.remove(launcher); + applet.repaint(); + callInitCallback(); } - if ((al != null) && (al.getHeight() > 0)) + } + + /** + * 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) { - dbgMsg("Successfully loaded file."); - newAlignFrame = new AlignFrame(al, applet, file, embedded); - if (initialAlignFrame == 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)) { - initialAlignFrame = newAlignFrame; + al2.alignAs(al1); + SplitFrame sf = new SplitFrame(af, af2); + sf.addToDisplay(embedded, JalviewLite.this); + return; } - // update the focus. - currentAlignFrame = newAlignFrame; - - if (protocol == jalview.io.AppletFormatAdapter.PASTE) + else { - newAlignFrame.setTitle("Sequences from " - + applet.getDocumentBase()); + String msg = "Could not map any sequence in " + af2.getTitle() + + " as " + + (al1.isNucleotide() ? "protein product" : "cDNA") + + " for " + af.getTitle(); + System.err.println(msg); } + } - newAlignFrame.statusBar.setText("Successfully loaded file " + file); - - String treeFile = applet.getParameter("tree"); - if (treeFile == null) - { - treeFile = applet.getParameter("treeFile"); - } + af.addToDisplay(embedded); + } - if (treeFile != null) + /** + * Read the alignment file (from URL, text 'paste', or archive by + * classloader). + * + * @return + */ + protected AlignFrame readAlignment(String fileParam) + { + if (fileParam == null) + { + return null; + } + String resolvedFile = resolveFileProtocol(fileParam); + AlignmentI al = null; + try + { + FileFormatI format = new IdentifyFile().identify(resolvedFile, + protocol); + dbgMsg("File identified as '" + format + "'"); + al = new AppletFormatAdapter().readFile(resolvedFile, protocol, + format); + if ((al != null) && (al.getHeight() > 0)) { - try - { - treeFile = setProtocolState(treeFile); - /* - * if (inArchive(treeFile)) { protocol = - * AppletFormatAdapter.CLASSLOADER; } else { protocol = - * AppletFormatAdapter.URL; treeFile = addProtocol(treeFile); } - */ - jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile, - protocol); - - fin.parse(); - - if (fin.getTree() != null) - { - newAlignFrame.loadTree(fin, treeFile); - dbgMsg("Successfuly imported tree."); - } - else - { - dbgMsg("Tree parameter did not resolve to a valid tree."); - } - } catch (Exception ex) + dbgMsg("Successfully loaded file."); + al.setDataset(null); + AlignFrame newAlignFrame = new AlignFrame(al, applet, + resolvedFile, embedded, false); + newAlignFrame.setTitle(resolvedFile); + if (initialAlignFrame == null) { - ex.printStackTrace(); + initialAlignFrame = newAlignFrame; } - } - - String param = applet.getParameter("features"); - if (param != null) - { - param = setProtocolState(param); + // update the focus. + currentAlignFrame = newAlignFrame; - newAlignFrame.parseFeaturesFile(param, protocol); - } - - param = applet.getParameter("showFeatureSettings"); - if (param != null && param.equalsIgnoreCase("true")) - { - newAlignFrame.viewport.showSequenceFeatures(true); - new FeatureSettings(newAlignFrame.alignPanel); - } - - param = applet.getParameter("annotations"); - if (param != null) - { - param = setProtocolState(param); - - if (new AnnotationFile().readAnnotationFile( - newAlignFrame.viewport.getAlignment(), param, protocol)) + if (protocol == DataSourceType.PASTE) { - newAlignFrame.alignPanel.fontChanged(); - newAlignFrame.alignPanel.setScrollValues(0, 0); - } - else - { - System.err - .println("Annotations were not added from annotation file '" - + param + "'"); + newAlignFrame.setTitle(MessageManager + .formatMessage("label.sequences_from", new Object[] + { applet.getDocumentBase().toString() })); } - } + newAlignFrame.statusBar.setText(MessageManager.formatMessage( + "label.successfully_loaded_file", new Object[] + { resolvedFile })); - param = applet.getParameter("jnetfile"); - if (param != null) - { - try - { - param = setProtocolState(param); - jalview.io.JPredFile predictions = new jalview.io.JPredFile( - param, protocol); - JnetAnnotationMaker.add_annotation(predictions, - newAlignFrame.viewport.getAlignment(), 0, false); // false==do - // not - // add - // sequence - // profile - // from - // concise - // output - newAlignFrame.alignPanel.fontChanged(); - newAlignFrame.alignPanel.setScrollValues(0, 0); - } catch (Exception ex) - { - ex.printStackTrace(); - } + return newAlignFrame; } - /* - * Undocumented for 2.6 - * - related to JAL-434 - */ - applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles", - false)); - /* - * - * - * - * - * - */ - - int pdbFileCount = 0; - // Accumulate pdbs here if they are heading for the same view (if - // alignPdbStructures is true) - Vector pdbs = new Vector(); - // create a lazy matcher if we're asked to - jalview.analysis.SequenceIdMatcher matcher = (applet.getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher( - newAlignFrame.getAlignViewport().getAlignment().getSequencesArray()) : null; - - do + } catch (java.io.IOException ex) + { + dbgMsg("File load exception."); + ex.printStackTrace(); + if (debug) { - if (pdbFileCount > 0) - param = applet.getParameter("PDBFILE" + pdbFileCount); - else - param = applet.getParameter("PDBFILE"); - - if (param != null) + try { - PDBEntry pdb = new PDBEntry(); - - String seqstring; - SequenceI[] seqs = null; - String[] chains = null; - - StringTokenizer st = new StringTokenizer(param, " "); - - if (st.countTokens() < 2) - { - String sequence = applet.getParameter("PDBSEQ"); - if (sequence != null) - seqs = new SequenceI[] - { matcher==null ? (Sequence) newAlignFrame.getAlignViewport() - .getAlignment().findName(sequence) : matcher.findIdMatch(sequence) }; - - } - else - { - param = st.nextToken(); - Vector tmp = new Vector(); - Vector tmp2 = new Vector(); - - while (st.hasMoreTokens()) - { - seqstring = st.nextToken(); - StringTokenizer st2 = new StringTokenizer(seqstring, "="); - if (st2.countTokens() > 1) - { - // This is the chain - tmp2.addElement(st2.nextToken()); - seqstring = st2.nextToken(); - } - tmp.addElement(matcher==null ? (Sequence) newAlignFrame.getAlignViewport() - .getAlignment().findName(seqstring) : matcher.findIdMatch(seqstring)); - } - - seqs = new SequenceI[tmp.size()]; - tmp.copyInto(seqs); - if (tmp2.size() == tmp.size()) - { - chains = new String[tmp2.size()]; - tmp2.copyInto(chains); - } - } - param = setProtocolState(param); - - if (// !jmolAvailable - // && - protocol == AppletFormatAdapter.CLASSLOADER) - { - // 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) + FileParse fp = new FileParse(resolvedFile, protocol); + String ln = null; + dbgMsg(">>>Dumping contents of '" + resolvedFile + "' " + "(" + + protocol + ")"); + while ((ln = fp.nextLine()) != null) { - for (int i = 0; i < seqs.length; i++) - { - if (seqs[i] != null) - { - ((Sequence) seqs[i]).addPDBId(pdb); - } - else - { - if (JalviewLite.debug) - { - // this may not really be a problem but we give a warning - // anyway - System.err - .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence " - + i + ")"); - } - } - } - - if (!alignPdbStructures) - { - newAlignFrame.newStructureView(applet, pdb, seqs, chains, - protocol); - } - else - { - pdbs.addElement(new Object[] - { pdb, seqs, chains, new String(protocol) }); - } + dbgMsg(ln); } - } - - pdbFileCount++; - } while (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++) + dbgMsg(">>>Dump finished."); + } catch (Exception e) { - 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]; + System.err.println( + "Exception when trying to dump the content of the file parameter."); + e.printStackTrace(); } - newAlignFrame.alignedStructureView(applet, pdb, seqs, chains, - protocols); - - } - // /////////////////////////// - // modify display of features - // - // hide specific groups - param = applet.getParameter("hidefeaturegroups"); - if (param != null) - { - applet.setFeatureGroupStateOn(newAlignFrame, param, false); - } - // show specific groups - param = applet.getParameter("showfeaturegroups"); - if (param != null) - { - applet.setFeatureGroupStateOn(newAlignFrame, param, true); } } - else - { - fileFound = false; - applet.remove(launcher); - applet.repaint(); - } - } - - /** - * 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; - } + return null; } - String addProtocol(String file) - { - if (file.indexOf("://") == -1) - { - file = applet.getCodeBase() + file; - if (debug) - { - System.err.println("Prepended codebase for resource: '" + file - + "'"); - } - } - - return file; - } } /** @@ -1832,8 +2054,8 @@ public class JalviewLite extends Applet { return initialAlignFrame; } - System.err - .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use."); + System.err.println( + "Implementation error: Jalview Applet API cannot work out which AlignFrame to use."); return null; } @@ -1845,69 +2067,20 @@ public class JalviewLite extends Applet // IDS include pipes. /** - * parse the string into a list - * - * @param list - * @return elements separated by separator + * set to enable the URL based javascript execution mechanism */ - public String[] separatorListToArray(String list) - { - return separatorListToArray(list, separator); - } + private boolean jsfallbackEnabled = false; /** * parse the string into a list * * @param list - * @param separator * @return elements separated by separator */ - public String[] separatorListToArray(String list, String separator) + @Override + public String[] separatorListToArray(String list) { - // 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; + return JalviewAppLoader.separatorListToArray(list, separator); } /** @@ -1916,133 +2089,118 @@ public class JalviewLite extends Applet * @param list * @return concatenated string */ + @Override public String arrayToSeparatorList(String[] list) { - return arrayToSeparatorList(list, separator); + return JalviewAppLoader.arrayToSeparatorList(list, separator); } - /** - * concatenate the list with separator + /* + * (non-Javadoc) * - * @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; - } - - /** - * @return - * @see jalview.appletgui.AlignFrame#getFeatureGroups() + * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups() */ + @Override public String getFeatureGroups() { - String lst = arrayToSeparatorList(getDefaultTargetFrame() - .getFeatureGroups()); + String lst = arrayToSeparatorList( + getDefaultTargetFrame().getFeatureGroups()); 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) + @Override + public String getFeatureGroupsOn(AlignFrameI alf) { - String lst = arrayToSeparatorList(alf.getFeatureGroups()); + String lst = arrayToSeparatorList( + ((AlignFrame) alf).getFeatureGroups()); return lst; } - /** - * @param visible - * @return - * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean) + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean) */ + @Override public String getFeatureGroupsOfState(boolean visible) { - return arrayToSeparatorList(getDefaultTargetFrame() - .getFeatureGroupsOfState(visible)); + return arrayToSeparatorList( + getDefaultTargetFrame().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) + @Override + public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible) { - return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible)); + return arrayToSeparatorList( + ((AlignFrame) 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) + @Override + public void setFeatureGroupStateOn(final AlignFrameI alf, + final String groups, boolean state) { - boolean st = state;// !(state==null || state.equals("") || + final boolean st = state;// !(state==null || state.equals("") || // state.toLowerCase().equals("false")); - alf.setFeatureGroupState(separatorListToArray(groups), st); + java.awt.EventQueue.invokeLater(new Runnable() + { + @Override + public void run() + { + ((AlignFrame) alf) + .setFeatureGroupState(separatorListToArray(groups), st); + } + }); } + /* + * (non-Javadoc) + * + * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupState(java.lang.String, + * boolean) + */ + @Override public void setFeatureGroupState(String groups, boolean state) { setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state); } - /** - * List separator string + /* + * (non-Javadoc) * - * @return the separator + * @see jalview.bin.JalviewLiteJsApi#getSeparator() */ + @Override public String getSeparator() { return separator; } - /** - * List separator string + /* + * (non-Javadoc) * - * @param separator - * the separator to set. empty string will reset separator to default + * @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String) */ + @Override public void setSeparator(String separator) { if (separator == null || separator.length() < 1) @@ -2067,6 +2225,7 @@ public class JalviewLite extends Applet * the value to return otherwise * @return true or false */ + @Override public boolean getDefaultParameter(String name, boolean def) { String stn; @@ -2074,36 +2233,29 @@ public class JalviewLite extends Applet { return def; } - if (stn.toLowerCase().equals("true")) + if (TRUE.equalsIgnoreCase(stn)) { return true; } return false; } - /** - * bind a pdb file to a sequence in the given alignFrame. + /* + * (non-Javadoc) * - * @param alFrame - * - null or specific alignFrame. This specifies the dataset that - * will be searched for a seuqence called sequenceId - * @param sequenceId - * - sequenceId within the dataset. - * @param pdbEntryString - * - the short name for the PDB file - * @param pdbFile - * - pdb file - either a URL or a valid PDB file. - * @return true if binding was as success TODO: consider making an exception - * structure for indicating when PDB parsing or seqeunceId location - * fails. - */ - public boolean addPdbFile(AlignFrame alFrame, String sequenceId, + * @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame, + * java.lang.String, java.lang.String, java.lang.String) + */ + @Override + public boolean addPdbFile(AlignFrameI alFrame, String sequenceId, String pdbEntryString, String pdbFile) { - return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile); + return ((AlignFrame) alFrame).addPdbFile(sequenceId, pdbEntryString, + pdbFile); } - protected void setAlignPdbStructures(boolean alignPdbStructures) + @Override + public void setAlignPdbStructures(boolean alignPdbStructures) { this.alignPdbStructures = alignPdbStructures; } @@ -2113,26 +2265,330 @@ public class JalviewLite extends Applet return alignPdbStructures; } + @Override public void start() { - callInitCallback(); + // callInitCallback(); + } + + private Hashtable jshashes = new Hashtable<>(); + + private Hashtable> jsmessages = new Hashtable<>(); + + + @Override + public Hashtable getJSHashes() + { + return jshashes; } + @Override + public Hashtable> getJSMessages() + { + return jsmessages; + } + + private Vector jsExecQueue = new Vector<>(); + + @Override + public Vector getJsExecQueue(JSFunctionExec exec) + { + jsFunctionExec = exec; + return jsExecQueue; + } + + // public void setExecutor(JSFunctionExec jsFunctionExec2) + // { + // jsFunctionExec = jsFunctionExec2; + // } + /** - * bind structures in a viewer to any matching sequences in an alignFrame (use - * sequenceIds to limit scope of search to specific sequences) + * return the given colour value parameter or the given default if parameter + * not given * - * @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) { + * @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 = ColorUtils.parseColourString(colprop); + if (col == null) + { + System.err.println("Couldn't parse '" + colprop + "' as a colour for " + + colparam); + } + 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"); + } + + /** + * open a URL in the browser - resolving it according to relative refs and + * coping with javascript: protocol if necessary. * - * if (sequenceIds != null && sequenceIds.length() > 0) { return - * alFrame.addStructureViewInstance(viewer, - * separatorListToArray(sequenceIds)); } else { return - * alFrame.addStructureViewInstance(viewer, null); } // return null; } + * @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 = JalviewAppLoader.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(); + } + } + + @Override + public AlignViewportI getViewport() + { + return loaderFrame.getAlignViewport(); + } + + @Override + public void newStructureView(PDBEntry pdb, SequenceI[] seqs, + String[] chains, DataSourceType protocol) + { + loaderFrame.newStructureView(this, pdb, seqs, chains, + protocol); + } + + @Override + public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs, + String[][] chains, String[] protocols) + { + loaderFrame.alignedStructureView(this, pdb, seqs, chains, protocols); + } + + @Override + public void updateForAnnotations() + { + loaderFrame.alignPanel.fontChanged(); + loaderFrame.alignPanel.setScrollValues(0, 0); + } + + @Override + public void setFeatureGroupState(String[] groups, boolean state) + { + loaderFrame.setFeatureGroupState(groups, state); + } + + @Override + public boolean parseFeaturesFile(String param, DataSourceType protocol) + { + return loaderFrame.parseFeaturesFile(param, protocol); + } + + @Override + public void newFeatureSettings() + { + getViewport().setShowSequenceFeatures(true); + new FeatureSettings(loaderFrame.alignPanel); + } + + @Override + public boolean loadScoreFile(String sScoreFile) throws IOException + { + return loaderFrame.loadScoreFile(sScoreFile); + } + + @Override + public void loadTree(NewickFile tree, String treeFile) throws IOException + { + loaderFrame.loadTree(tree, treeFile); + } + + @Override + public boolean isJsfallbackEnabled() + { + return jsfallbackEnabled; + } + + @Override + public JSObject getJSObject() + { + return JSObject.getWindow(this); + } + + @Override + public void updateColoursFromMouseOver(Object source, + MouseOverStructureListener listener) + { + } + + @Override + public Object[] getSelectionForListener(SequenceGroup seqsel, ColumnSelection colsel, + HiddenColumns hidden, SelectionSource source, Object alignFrame) + { + // System.err.println("Testing selection event relay to + // jsfunction:"+_listener); + String setid = ""; + AlignFrame src = (AlignFrame) alignFrame; + if (source != null) + { + if (source instanceof jalview.appletgui.AlignViewport + && ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame.viewport == source) + { + // should be valid if it just generated an event! + src = ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame; + + } + } + String[] seqs = new String[] {}; + String[] cols = new String[] {}; + int strt = 0, end = (src == null) ? -1 + : src.alignPanel.av.getAlignment().getWidth(); + if (seqsel != null && seqsel.getSize() > 0) + { + seqs = new String[seqsel.getSize()]; + for (int i = 0; i < seqs.length; i++) + { + seqs[i] = seqsel.getSequenceAt(i).getName(); + } + if (strt < seqsel.getStartRes()) + { + strt = seqsel.getStartRes(); + } + if (end == -1 || end > seqsel.getEndRes()) + { + end = seqsel.getEndRes(); + } + } + if (colsel != null && !colsel.isEmpty()) + { + if (end == -1) + { + end = colsel.getMax() + 1; + } + cols = new String[colsel.getSelected().size()]; + for (int i = 0; i < cols.length; i++) + { + cols[i] = "" + (1 + colsel.getSelected().get(i).intValue()); + } + } + else + { + if (seqsel != null && seqsel.getSize() > 0) + { + // send a valid range, otherwise we send the empty selection + cols = new String[2]; + cols[0] = "" + (1 + strt) + "-" + (1 + end); + } + } + return new Object[] + { src, setid, arrayToSeparatorList(seqs), arrayToSeparatorList(cols) }; + } + + @Override + public String getJsMessage(String messageclass, String viewId) + { + return JSFunctionExec.getJsMessage(messageclass, viewId, this); + } + + @Override + public Object getFrameForSource(VamsasSource source) + { + if (source != null) + { + if (source instanceof jalview.appletgui.AlignViewport + && ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame.viewport == source) + { + // should be valid if it just generated an event! + return ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame; + + } + // TODO: ensure that if '_af' is specified along with a handler + // function, then only events from that alignFrame are sent to that + // function + } + return null; + } + + @Override + public FeatureRenderer getNewFeatureRenderer(AlignViewportI vp) + { + return new jalview.appletgui.FeatureRenderer((AlignmentViewport) vp); + } + + @Override + public String getSelectedSequencesAsAlignment(String format, + boolean suffix) + { + // TODO Auto-generated method stub + return null; + } + + @Override + public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf, + String format, boolean suffix) + { + // TODO Auto-generated method stub + return null; + } + + // /** + // * 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; } + // */ }