2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentUtils;
24 import jalview.api.StructureSelectionManagerProvider;
25 import jalview.appletgui.AlignFrame;
26 import jalview.appletgui.AlignViewport;
27 import jalview.appletgui.EmbmenuFrame;
28 import jalview.appletgui.FeatureSettings;
29 import jalview.appletgui.SplitFrame;
30 import jalview.datamodel.Alignment;
31 import jalview.datamodel.AlignmentI;
32 import jalview.datamodel.AlignmentOrder;
33 import jalview.datamodel.ColumnSelection;
34 import jalview.datamodel.PDBEntry;
35 import jalview.datamodel.Sequence;
36 import jalview.datamodel.SequenceGroup;
37 import jalview.datamodel.SequenceI;
38 import jalview.io.AnnotationFile;
39 import jalview.io.AppletFormatAdapter;
40 import jalview.io.DataSourceType;
41 import jalview.io.FileFormat;
42 import jalview.io.FileFormatI;
43 import jalview.io.FileParse;
44 import jalview.io.IdentifyFile;
45 import jalview.io.JPredFile;
46 import jalview.io.JnetAnnotationMaker;
47 import jalview.io.NewickFile;
48 import jalview.javascript.JSFunctionExec;
49 import jalview.javascript.JalviewLiteJsApi;
50 import jalview.javascript.JsCallBack;
51 import jalview.javascript.MouseOverStructureListener;
52 import jalview.structure.SelectionListener;
53 import jalview.structure.StructureSelectionManager;
54 import jalview.util.HttpUtils;
55 import jalview.util.MessageManager;
57 import java.applet.Applet;
58 import java.awt.Button;
59 import java.awt.Color;
60 import java.awt.Component;
61 import java.awt.EventQueue;
63 import java.awt.Frame;
64 import java.awt.Graphics;
65 import java.awt.event.ActionEvent;
66 import java.awt.event.WindowAdapter;
67 import java.awt.event.WindowEvent;
68 import java.io.BufferedReader;
69 import java.io.IOException;
70 import java.io.InputStreamReader;
72 import java.util.ArrayList;
73 import java.util.Hashtable;
74 import java.util.List;
75 import java.util.StringTokenizer;
76 import java.util.Vector;
78 import netscape.javascript.JSObject;
81 * Jalview Applet. Runs in Java 1.18 runtime
84 * @version $Revision: 1.92 $
86 public class JalviewLite extends Applet implements
87 StructureSelectionManagerProvider, JalviewLiteJsApi
90 private static final String TRUE = "true";
92 private static final String FALSE = "false";
94 public StructureSelectionManager getStructureSelectionManager()
96 return StructureSelectionManager.getStructureSelectionManager(this);
99 // /////////////////////////////////////////
100 // The following public methods may be called
101 // externally, eg via javascript in HTML page
105 * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences()
108 public String getSelectedSequences()
110 return getSelectedSequencesFrom(getDefaultTargetFrame());
116 * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
119 public String getSelectedSequences(String sep)
121 return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);
128 * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
132 public String getSelectedSequencesFrom(AlignFrame alf)
134 return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);
141 * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
142 * .AlignFrame, java.lang.String)
145 public String getSelectedSequencesFrom(AlignFrame alf, String sep)
147 StringBuffer result = new StringBuffer("");
148 if (sep == null || sep.length() == 0)
150 sep = separator; // "+0x00AC;
152 if (alf.viewport.getSelectionGroup() != null)
154 SequenceI[] seqs = alf.viewport.getSelectionGroup()
155 .getSequencesInOrder(alf.viewport.getAlignment());
157 for (int i = 0; i < seqs.length; i++)
159 result.append(seqs[i].getName());
164 return result.toString();
170 * @see jalview.bin.JalviewLiteJsApi#highlight(java.lang.String,
171 * java.lang.String, java.lang.String)
174 public void highlight(String sequenceId, String position,
175 String alignedPosition)
177 highlightIn(getDefaultTargetFrame(), sequenceId, position,
184 * @see jalview.bin.JalviewLiteJsApi#highlightIn(jalview.appletgui.AlignFrame,
185 * java.lang.String, java.lang.String, java.lang.String)
188 public void highlightIn(final AlignFrame alf, final String sequenceId,
189 final String position, final String alignedPosition)
191 // TODO: could try to highlight in all alignments if alf==null
192 jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
193 alf.viewport.getAlignment().getSequencesArray());
194 final SequenceI sq = matcher.findIdMatch(sequenceId);
200 apos = new Integer(position).intValue();
202 } catch (NumberFormatException ex)
206 final StructureSelectionManagerProvider me = this;
207 final int pos = apos;
208 // use vamsas listener to broadcast to all listeners in scope
209 if (alignedPosition != null
210 && (alignedPosition.trim().length() == 0 || alignedPosition
211 .toLowerCase().indexOf("false") > -1))
213 java.awt.EventQueue.invokeLater(new Runnable()
218 StructureSelectionManager.getStructureSelectionManager(me)
219 .mouseOverVamsasSequence(sq, sq.findIndex(pos), null);
225 java.awt.EventQueue.invokeLater(new Runnable()
230 StructureSelectionManager.getStructureSelectionManager(me)
231 .mouseOverVamsasSequence(sq, pos, null);
241 * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
245 public void select(String sequenceIds, String columns)
247 selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator);
253 * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
254 * java.lang.String, java.lang.String)
257 public void select(String sequenceIds, String columns, String sep)
259 selectIn(getDefaultTargetFrame(), sequenceIds, columns, sep);
265 * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
266 * java.lang.String, java.lang.String)
269 public void selectIn(AlignFrame alf, String sequenceIds, String columns)
271 selectIn(alf, sequenceIds, columns, separator);
277 * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
278 * java.lang.String, java.lang.String, java.lang.String)
281 public void selectIn(final AlignFrame alf, String sequenceIds,
282 String columns, String sep)
284 if (sep == null || sep.length() == 0)
292 System.err.println("Selecting region using separator string '"
297 String[] ids = separatorListToArray(sequenceIds, sep);
298 String[] cols = separatorListToArray(columns, sep);
299 final SequenceGroup sel = new SequenceGroup();
300 final ColumnSelection csel = new ColumnSelection();
301 AlignmentI al = alf.viewport.getAlignment();
302 jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
303 alf.viewport.getAlignment().getSequencesArray());
304 int start = 0, end = al.getWidth(), alw = al.getWidth();
305 boolean seqsfound = true;
306 if (ids != null && ids.length > 0)
309 for (int i = 0; i < ids.length; i++)
311 if (ids[i].trim().length() == 0)
315 SequenceI sq = matcher.findIdMatch(ids[i]);
319 sel.addSequence(sq, false);
323 boolean inseqpos = false;
324 if (cols != null && cols.length > 0)
326 boolean seset = false;
327 for (int i = 0; i < cols.length; i++)
329 String cl = cols[i].trim();
330 if (cl.length() == 0)
335 if ((p = cl.indexOf("-")) > -1)
337 int from = -1, to = -1;
340 from = new Integer(cl.substring(0, p)).intValue();
342 } catch (NumberFormatException ex)
345 .println("ERROR: Couldn't parse first integer in range element column selection string '"
346 + cl + "' - format is 'from-to'");
351 to = new Integer(cl.substring(p + 1)).intValue();
353 } catch (NumberFormatException ex)
356 .println("ERROR: Couldn't parse second integer in range element column selection string '"
357 + cl + "' - format is 'from-to'");
360 if (from >= 0 && to >= 0)
377 // comment to prevent range extension
387 for (int r = from; r <= to; r++)
389 if (r >= 0 && r < alw)
396 System.err.println("Range '" + cl + "' deparsed as [" + from
402 System.err.println("ERROR: Invalid Range '" + cl
403 + "' deparsed as [" + from + "," + to + "]");
411 r = new Integer(cl).intValue();
413 } catch (NumberFormatException ex)
415 if (cl.toLowerCase().equals("sequence"))
417 // we are in the dataset sequence's coordinate frame.
423 .println("ERROR: Couldn't parse integer from point selection element of column selection string '"
428 if (r >= 0 && r <= alw)
438 // comment to prevent range extension
451 System.err.println("Point selection '" + cl
452 + "' deparsed as [" + r + "]");
457 System.err.println("ERROR: Invalid Point selection '" + cl
458 + "' deparsed as [" + r + "]");
465 // we only propagate the selection when it was the null selection, or the
466 // given sequences were found in the alignment.
467 if (inseqpos && sel.getSize() > 0)
469 // assume first sequence provides reference frame ?
470 SequenceI rs = sel.getSequenceAt(0);
471 start = rs.findIndex(start);
472 end = rs.findIndex(end);
473 List<Integer> cs = new ArrayList<Integer>(csel.getSelected());
475 for (Integer selectedCol : cs)
477 csel.addElement(rs.findIndex(selectedCol));
480 sel.setStartRes(start);
482 EventQueue.invokeLater(new Runnable()
487 alf.select(sel, csel);
497 * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignment(java.lang.
498 * String, java.lang.String)
501 public String getSelectedSequencesAsAlignment(String format, String suffix)
503 return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(),
511 * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignmentFrom(jalview
512 * .appletgui.AlignFrame, java.lang.String, java.lang.String)
515 public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
516 String format, String suffix)
520 FileFormatI theFormat = FileFormat.valueOf(format);
521 boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
522 if (alf.viewport.getSelectionGroup() != null)
524 // JBPNote: getSelectionAsNewSequence behaviour has changed - this
525 // method now returns a full copy of sequence data
526 // TODO consider using getSequenceSelection instead here
527 String reply = new AppletFormatAdapter().formatSequences(theFormat,
528 new Alignment(alf.viewport.getSelectionAsNewSequence()),
532 } catch (IllegalArgumentException ex)
534 ex.printStackTrace();
535 return "Error retrieving alignment, possibly invalid format specifier: "
544 * @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder()
547 public String getAlignmentOrder()
549 return getAlignmentOrderFrom(getDefaultTargetFrame());
556 * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
560 public String getAlignmentOrderFrom(AlignFrame alf)
562 return getAlignmentOrderFrom(alf, separator);
569 * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
570 * , java.lang.String)
573 public String getAlignmentOrderFrom(AlignFrame alf, String sep)
575 AlignmentI alorder = alf.getAlignViewport().getAlignment();
576 String[] order = new String[alorder.getHeight()];
577 for (int i = 0; i < order.length; i++)
579 order[i] = alorder.getSequenceAt(i).getName();
581 return arrayToSeparatorList(order);
587 * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
591 public String orderBy(String order, String undoName)
593 return orderBy(order, undoName, separator);
599 * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
600 * java.lang.String, java.lang.String)
603 public String orderBy(String order, String undoName, String sep)
605 return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep);
612 * jalview.bin.JalviewLiteJsApi#orderAlignmentBy(jalview.appletgui.AlignFrame,
613 * java.lang.String, java.lang.String, java.lang.String)
616 public String orderAlignmentBy(AlignFrame alf, String order,
617 String undoName, String sep)
619 String[] ids = separatorListToArray(order, sep);
620 SequenceI[] sqs = null;
621 if (ids != null && ids.length > 0)
623 jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
624 alf.viewport.getAlignment().getSequencesArray());
626 sqs = new SequenceI[ids.length];
627 for (int i = 0; i < ids.length; i++)
629 if (ids[i].trim().length() == 0)
633 SequenceI sq = matcher.findIdMatch(ids[i]);
641 SequenceI[] sqq = new SequenceI[s];
642 System.arraycopy(sqs, 0, sqq, 0, s);
655 final AlignmentOrder aorder = new AlignmentOrder(sqs);
657 if (undoName != null && undoName.trim().length() == 0)
661 final String _undoName = undoName;
662 // TODO: deal with synchronization here: cannot raise any events until after
663 // this has returned.
664 return alf.sortBy(aorder, _undoName) ? TRUE : "";
670 * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String)
673 public String getAlignment(String format)
675 return getAlignmentFrom(getDefaultTargetFrame(), format, TRUE);
682 * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
686 public String getAlignmentFrom(AlignFrame alf, String format)
688 return getAlignmentFrom(alf, format, TRUE);
694 * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String,
698 public String getAlignment(String format, String suffix)
700 return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);
707 * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
708 * java.lang.String, java.lang.String)
711 public String getAlignmentFrom(AlignFrame alf, String format,
716 boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
718 FileFormatI theFormat = FileFormat.valueOf(format);
719 String reply = new AppletFormatAdapter().formatSequences(theFormat,
720 alf.viewport.getAlignment(), seqlimits);
722 } catch (IllegalArgumentException ex)
724 ex.printStackTrace();
725 return "Error retrieving alignment, possibly invalid format specifier: "
733 * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
736 public void loadAnnotation(String annotation)
738 loadAnnotationFrom(getDefaultTargetFrame(), annotation);
745 * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
746 * , java.lang.String)
749 public void loadAnnotationFrom(AlignFrame alf, String annotation)
751 if (new AnnotationFile().annotateAlignmentView(alf.getAlignViewport(),
752 annotation, DataSourceType.PASTE))
754 alf.alignPanel.fontChanged();
755 alf.alignPanel.setScrollValues(0, 0);
759 alf.parseFeaturesFile(annotation, DataSourceType.PASTE);
766 * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
769 public void loadFeatures(String features, boolean autoenabledisplay)
771 loadFeaturesFrom(getDefaultTargetFrame(), features, autoenabledisplay);
778 * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
779 * , java.lang.String)
782 public boolean loadFeaturesFrom(AlignFrame alf, String features,
783 boolean autoenabledisplay)
785 return alf.parseFeaturesFile(features, DataSourceType.PASTE,
792 * @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String)
795 public String getFeatures(String format)
797 return getFeaturesFrom(getDefaultTargetFrame(), format);
804 * jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame,
808 public String getFeaturesFrom(AlignFrame alf, String format)
810 return alf.outputFeatures(false, format);
816 * @see jalview.bin.JalviewLiteJsApi#getAnnotation()
819 public String getAnnotation()
821 return getAnnotationFrom(getDefaultTargetFrame());
828 * jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame
832 public String getAnnotationFrom(AlignFrame alf)
834 return alf.outputAnnotations(false);
840 * @see jalview.bin.JalviewLiteJsApi#newView()
843 public AlignFrame newView()
845 return newViewFrom(getDefaultTargetFrame());
851 * @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String)
854 public AlignFrame newView(String name)
856 return newViewFrom(getDefaultTargetFrame(), name);
862 * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame)
865 public AlignFrame newViewFrom(AlignFrame alf)
867 return alf.newView(null);
873 * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame,
877 public AlignFrame newViewFrom(AlignFrame alf, String name)
879 return alf.newView(name);
885 * @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String,
889 public AlignFrame loadAlignment(String text, String title)
891 AlignmentI al = null;
895 FileFormatI format = new IdentifyFile().identify(text,
896 DataSourceType.PASTE);
897 al = new AppletFormatAdapter().readFile(text, DataSourceType.PASTE,
899 if (al.getHeight() > 0)
901 return new AlignFrame(al, this, title, false);
903 } catch (IOException ex)
905 ex.printStackTrace();
913 * @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String)
916 public void setMouseoverListener(String listener)
918 setMouseoverListener(currentAlignFrame, listener);
921 private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<jalview.javascript.JSFunctionExec>();
927 * jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame
928 * , java.lang.String)
931 public void setMouseoverListener(AlignFrame af, String listener)
933 if (listener != null)
935 listener = listener.trim();
936 if (listener.length() == 0)
939 .println("jalview Javascript error: Ignoring empty function for mouseover listener.");
943 jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener(
945 javascriptListeners.addElement(mol);
946 StructureSelectionManager.getStructureSelectionManager(this)
947 .addStructureViewerListener(mol);
950 System.err.println("Added a mouseover listener for "
951 + ((af == null) ? "All frames" : "Just views for "
952 + af.getAlignViewport().getSequenceSetId()));
953 System.err.println("There are now " + javascriptListeners.size()
954 + " listeners in total.");
961 * @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String)
964 public void setSelectionListener(String listener)
966 setSelectionListener(null, listener);
973 * jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame
974 * , java.lang.String)
977 public void setSelectionListener(AlignFrame af, String listener)
979 if (listener != null)
981 listener = listener.trim();
982 if (listener.length() == 0)
985 .println("jalview Javascript error: Ignoring empty function for selection listener.");
989 jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender(
991 javascriptListeners.addElement(mol);
992 StructureSelectionManager.getStructureSelectionManager(this)
993 .addSelectionListener(mol);
996 System.err.println("Added a selection listener for "
997 + ((af == null) ? "All frames" : "Just views for "
998 + af.getAlignViewport().getSequenceSetId()));
999 System.err.println("There are now " + javascriptListeners.size()
1000 + " listeners in total.");
1005 * Callable from javascript to register a javascript function to pass events
1006 * to a structure viewer.
1009 * the name of a javascript function
1011 * a token separated list of PDB file names listened for
1012 * @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String,
1016 public void setStructureListener(String listener, String modelSet)
1018 if (listener != null)
1020 listener = listener.trim();
1021 if (listener.length() == 0)
1024 .println("jalview Javascript error: Ignoring empty function for selection listener.");
1028 MouseOverStructureListener mol = new MouseOverStructureListener(this,
1029 listener, separatorListToArray(modelSet));
1030 javascriptListeners.addElement(mol);
1031 StructureSelectionManager.getStructureSelectionManager(this)
1032 .addStructureViewerListener(mol);
1035 System.err.println("Added a javascript structure viewer listener '"
1037 System.err.println("There are now " + javascriptListeners.size()
1038 + " listeners in total.");
1046 * jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui
1047 * .AlignFrame, java.lang.String)
1050 public void removeJavascriptListener(AlignFrame af, String listener)
1052 if (listener != null)
1054 listener = listener.trim();
1055 if (listener.length() == 0)
1060 boolean rprt = false;
1061 for (int ms = 0, msSize = javascriptListeners.size(); ms < msSize;)
1063 Object lstn = javascriptListeners.elementAt(ms);
1064 JsCallBack lstner = (JsCallBack) lstn;
1065 if ((af == null || lstner.getAlignFrame() == af)
1066 && (listener == null || lstner.getListenerFunction().equals(
1069 javascriptListeners.removeElement(lstner);
1071 if (lstner instanceof SelectionListener)
1073 StructureSelectionManager.getStructureSelectionManager(this)
1074 .removeSelectionListener((SelectionListener) lstner);
1078 StructureSelectionManager.getStructureSelectionManager(this)
1079 .removeStructureViewerListener(lstner, null);
1084 System.err.println("Removed listener '" + listener + "'");
1094 System.err.println("There are now " + javascriptListeners.size()
1095 + " listeners in total.");
1102 System.err.println("Applet " + getName() + " stop().");
1107 public void destroy()
1109 System.err.println("Applet " + getName() + " destroy().");
1113 private void tidyUp()
1116 if (currentAlignFrame != null && currentAlignFrame.viewport != null
1117 && currentAlignFrame.viewport.applet != null)
1119 AlignViewport av = currentAlignFrame.viewport;
1120 currentAlignFrame.closeMenuItem_actionPerformed();
1122 currentAlignFrame = null;
1124 if (javascriptListeners != null)
1126 while (javascriptListeners.size() > 0)
1128 jalview.javascript.JSFunctionExec mol = javascriptListeners
1130 javascriptListeners.removeElement(mol);
1131 if (mol instanceof SelectionListener)
1133 StructureSelectionManager.getStructureSelectionManager(this)
1134 .removeSelectionListener((SelectionListener) mol);
1138 StructureSelectionManager.getStructureSelectionManager(this)
1139 .removeStructureViewerListener(mol, null);
1144 if (jsFunctionExec != null)
1146 jsFunctionExec.stopQueue();
1147 jsFunctionExec.jvlite = null;
1149 initialAlignFrame = null;
1150 jsFunctionExec = null;
1151 javascriptListeners = null;
1152 StructureSelectionManager.release(this);
1155 private jalview.javascript.JSFunctionExec jsFunctionExec;
1160 * @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String,
1161 * java.lang.String, java.lang.String)
1164 public void mouseOverStructure(final String pdbResNum,
1165 final String chain, final String pdbfile)
1167 final StructureSelectionManagerProvider me = this;
1168 java.awt.EventQueue.invokeLater(new Runnable()
1175 StructureSelectionManager.getStructureSelectionManager(me)
1176 .mouseOverStructure(new Integer(pdbResNum).intValue(),
1180 System.err.println("mouseOver for '" + pdbResNum
1181 + "' in chain '" + chain + "' in structure '" + pdbfile
1184 } catch (NumberFormatException e)
1186 System.err.println("Ignoring invalid residue number string '"
1198 * jalview.bin.JalviewLiteJsApi#scrollViewToIn(jalview.appletgui.AlignFrame,
1199 * java.lang.String, java.lang.String)
1202 public void scrollViewToIn(final AlignFrame alf, final String topRow,
1203 final String leftHandColumn)
1205 java.awt.EventQueue.invokeLater(new Runnable()
1212 alf.scrollTo(new Integer(topRow).intValue(), new Integer(
1213 leftHandColumn).intValue());
1215 } catch (Exception ex)
1217 System.err.println("Couldn't parse integer arguments (topRow='"
1218 + topRow + "' and leftHandColumn='" + leftHandColumn
1220 ex.printStackTrace();
1230 * jalview.javascript.JalviewLiteJsApi#scrollViewToRowIn(jalview.appletgui
1231 * .AlignFrame, java.lang.String)
1234 public void scrollViewToRowIn(final AlignFrame alf, final String topRow)
1237 java.awt.EventQueue.invokeLater(new Runnable()
1244 alf.scrollToRow(new Integer(topRow).intValue());
1246 } catch (Exception ex)
1248 System.err.println("Couldn't parse integer arguments (topRow='"
1250 ex.printStackTrace();
1261 * jalview.javascript.JalviewLiteJsApi#scrollViewToColumnIn(jalview.appletgui
1262 * .AlignFrame, java.lang.String)
1265 public void scrollViewToColumnIn(final AlignFrame alf,
1266 final String leftHandColumn)
1268 java.awt.EventQueue.invokeLater(new Runnable()
1276 alf.scrollToColumn(new Integer(leftHandColumn).intValue());
1278 } catch (Exception ex)
1281 .println("Couldn't parse integer arguments (leftHandColumn='"
1282 + leftHandColumn + "')");
1283 ex.printStackTrace();
1290 // //////////////////////////////////////////////
1291 // //////////////////////////////////////////////
1293 public static int lastFrameX = 200;
1295 public static int lastFrameY = 200;
1297 boolean fileFound = true;
1299 String file = "No file";
1301 String file2 = null;
1303 Button launcher = new Button(
1304 MessageManager.getString("label.start_jalview"));
1307 * The currentAlignFrame is static, it will change if and when the user
1308 * selects a new window. Note that it will *never* point back to the embedded
1309 * AlignFrame if the applet is started as embedded on the page and then
1310 * afterwards a new view is created.
1312 public AlignFrame currentAlignFrame = null;
1315 * This is the first frame to be displayed, and does not change. API calls
1316 * will default to this instance if currentAlignFrame is null.
1318 AlignFrame initialAlignFrame = null;
1320 boolean embedded = false;
1322 private boolean checkForJmol = true;
1324 private boolean checkedForJmol = false; // ensure we don't check for jmol
1326 // every time the app is re-inited
1328 public boolean jmolAvailable = false;
1330 private boolean alignPdbStructures = false;
1333 * use an external structure viewer exclusively (no jmols or MCViews will be
1334 * opened by JalviewLite itself)
1336 public boolean useXtrnalSviewer = false;
1338 public static boolean debug = false;
1340 static String builddate = null, version = null, installation = null;
1342 private static void initBuildDetails()
1344 if (builddate == null)
1346 builddate = "unknown";
1348 installation = "applet";
1349 java.net.URL url = JalviewLite.class
1350 .getResource("/.build_properties");
1355 BufferedReader reader = new BufferedReader(new InputStreamReader(
1358 while ((line = reader.readLine()) != null)
1360 if (line.indexOf("VERSION") > -1)
1362 version = line.substring(line.indexOf("=") + 1);
1364 if (line.indexOf("BUILD_DATE") > -1)
1366 builddate = line.substring(line.indexOf("=") + 1);
1368 if (line.indexOf("INSTALLATION") > -1)
1370 installation = line.substring(line.indexOf("=") + 1);
1373 } catch (Exception ex)
1375 ex.printStackTrace();
1381 public static String getBuildDate()
1387 public static String getInstallation()
1390 return installation;
1393 public static String getVersion()
1399 // public JSObject scriptObject = null;
1402 * init method for Jalview Applet
1407 debug = TRUE.equalsIgnoreCase(getParameter("debug"));
1412 System.err.println("Applet context is '"
1413 + getAppletContext().getClass().toString() + "'");
1415 JSObject scriptObject = JSObject.getWindow(this);
1416 if (debug && scriptObject != null)
1418 System.err.println("Applet has Javascript callback support.");
1421 } catch (Exception ex)
1424 .println("Warning: No JalviewLite javascript callbacks available.");
1427 ex.printStackTrace();
1433 System.err.println("JalviewLite Version " + getVersion());
1434 System.err.println("Build Date : " + getBuildDate());
1435 System.err.println("Installation : " + getInstallation());
1437 String externalsviewer = getParameter("externalstructureviewer");
1438 if (externalsviewer != null)
1440 useXtrnalSviewer = externalsviewer.trim().toLowerCase().equals(TRUE);
1443 * if true disable the check for jmol
1445 String chkforJmol = getParameter("nojmol");
1446 if (chkforJmol != null)
1448 checkForJmol = !chkforJmol.equals(TRUE);
1451 * get the separator parameter if present
1453 String sep = getParameter("separator");
1456 if (sep.length() > 0)
1461 System.err.println("Separator set to '" + separator + "'");
1468 .getString("error.invalid_separator_parameter"));
1474 String param = getParameter("RGB");
1480 r = Integer.parseInt(param.substring(0, 2), 16);
1481 g = Integer.parseInt(param.substring(2, 4), 16);
1482 b = Integer.parseInt(param.substring(4, 6), 16);
1483 } catch (Exception ex)
1490 param = getParameter("label");
1493 launcher.setLabel(param);
1496 setBackground(new Color(r, g, b));
1498 file = getParameter("file");
1502 // Maybe the sequences are added as parameters
1503 StringBuffer data = new StringBuffer("PASTE");
1505 while ((file = getParameter("sequence" + i)) != null)
1507 data.append(file.toString() + "\n");
1510 if (data.length() > 5)
1512 file = data.toString();
1515 if (getDefaultParameter("enableSplitFrame", true))
1517 file2 = getParameter("file2");
1520 embedded = TRUE.equalsIgnoreCase(getParameter("embedded"));
1523 LoadingThread loader = new LoadingThread(file, file2, this);
1526 else if (file != null)
1529 * Start the applet immediately or show a button to start it
1531 if (FALSE.equalsIgnoreCase(getParameter("showbutton")))
1533 LoadingThread loader = new LoadingThread(file, file2, this);
1539 launcher.addActionListener(new java.awt.event.ActionListener()
1542 public void actionPerformed(ActionEvent e)
1544 LoadingThread loader = new LoadingThread(file, file2,
1553 // jalview initialisation with no alignment. loadAlignment() method can
1554 // still be called to open new alignments.
1561 private void initLiveConnect()
1563 // try really hard to get the liveConnect thing working
1564 boolean notFailed = false;
1566 while (!notFailed && tries < 10)
1570 System.err.println("LiveConnect request thread going to sleep.");
1574 Thread.sleep(700 * (1 + tries));
1575 } catch (InterruptedException q)
1581 System.err.println("LiveConnect request thread woken up.");
1585 JSObject scriptObject = JSObject.getWindow(this);
1586 if (scriptObject.eval("navigator") != null)
1590 } catch (Exception jsex)
1592 System.err.println("Attempt " + tries
1593 + " to access LiveConnect javascript failed.");
1598 private void callInitCallback()
1600 String initjscallback = getParameter("oninit");
1601 if (initjscallback == null)
1605 initjscallback = initjscallback.trim();
1606 if (initjscallback.length() > 0)
1608 JSObject scriptObject = null;
1611 scriptObject = JSObject.getWindow(this);
1612 } catch (Exception ex)
1616 // try really hard to let the browser plugin know we want liveconnect
1619 if (scriptObject != null)
1623 // do onInit with the JS executor thread
1624 new JSFunctionExec(this).executeJavascriptFunction(true,
1625 initjscallback, null, "Calling oninit callback '"
1626 + initjscallback + "'.");
1627 } catch (Exception e)
1629 System.err.println("Exception when executing _oninit callback '"
1630 + initjscallback + "'.");
1631 e.printStackTrace();
1636 System.err.println("Not executing _oninit callback '"
1637 + initjscallback + "' - no scripting allowed.");
1643 * Initialises and displays a new java.awt.Frame
1646 * java.awt.Frame to be displayed
1648 * title of new frame
1650 * width if new frame
1652 * height of new frame
1654 public static void addFrame(final Frame frame, String title, int width,
1657 frame.setLocation(lastFrameX, lastFrameY);
1660 frame.setSize(width, height);
1661 frame.setTitle(title);
1662 frame.addWindowListener(new WindowAdapter()
1665 public void windowClosing(WindowEvent e)
1667 if (frame instanceof AlignFrame)
1669 AlignViewport vp = ((AlignFrame) frame).viewport;
1670 ((AlignFrame) frame).closeMenuItem_actionPerformed();
1671 if (vp.applet.currentAlignFrame == frame)
1673 vp.applet.currentAlignFrame = null;
1681 if (frame instanceof EmbmenuFrame)
1683 ((EmbmenuFrame) frame).destroyMenus();
1685 frame.setMenuBar(null);
1690 public void windowActivated(WindowEvent e)
1692 if (frame instanceof AlignFrame)
1694 ((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame;
1697 System.err.println("Activated window " + frame);
1701 super.windowActivated(e);
1704 * Probably not necessary to do this - see TODO above. (non-Javadoc)
1707 * java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent
1710 * public void windowDeactivated(WindowEvent e) { if (currentAlignFrame ==
1711 * frame) { currentAlignFrame = null; if (debug) {
1712 * System.err.println("Deactivated window "+frame); } }
1713 * super.windowDeactivated(e); }
1716 frame.setVisible(true);
1720 * This paints the background surrounding the "Launch Jalview button" <br>
1722 * If file given in parameter not found, displays error message
1728 public void paint(Graphics g)
1732 g.setColor(new Color(200, 200, 200));
1733 g.setColor(Color.cyan);
1734 g.fillRect(0, 0, getSize().width, getSize().height);
1735 g.setColor(Color.red);
1737 MessageManager.getString("label.jalview_cannot_open_file"),
1739 g.drawString("\"" + file + "\"", 5, 30);
1743 g.setColor(Color.black);
1744 g.setFont(new Font("Arial", Font.BOLD, 24));
1745 g.drawString(MessageManager.getString("label.jalview_applet"), 50,
1746 getSize().height / 2 - 30);
1747 g.drawString(MessageManager.getString("label.loading_data") + "...",
1748 50, getSize().height / 2);
1753 * get all components associated with the applet of the given type
1758 public Vector getAppletWindow(Class class1)
1760 Vector wnds = new Vector();
1761 Component[] cmp = getComponents();
1764 for (int i = 0; i < cmp.length; i++)
1766 if (class1.isAssignableFrom(cmp[i].getClass()))
1768 wnds.addElement(cmp);
1775 class LoadJmolThread extends Thread
1777 private boolean running = false;
1782 if (running || checkedForJmol)
1791 if (!System.getProperty("java.version").startsWith("1.1"))
1793 Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
1794 jmolAvailable = true;
1799 .println("Jmol not available - Using MCview for structures");
1801 } catch (java.lang.ClassNotFoundException ex)
1807 jmolAvailable = false;
1811 .println("Skipping Jmol check. Will use MCView (probably)");
1814 checkedForJmol = true;
1818 public boolean notFinished()
1820 return running || !checkedForJmol;
1824 class LoadingThread extends Thread
1827 * State variable: protocol for access to file source
1829 DataSourceType protocol;
1831 String _file; // alignment file or URL spec
1833 String _file2; // second alignment file or URL spec
1837 private void dbgMsg(String msg)
1839 if (JalviewLite.debug)
1841 System.err.println(msg);
1846 * update the protocol state variable for accessing the datasource located
1850 * @return possibly updated datasource string
1852 public String resolveFileProtocol(String path)
1857 if (path.startsWith("PASTE"))
1859 protocol = DataSourceType.PASTE;
1860 return path.substring(5);
1866 if (path.indexOf("://") != -1)
1868 protocol = DataSourceType.URL;
1873 * try relative to document root
1875 URL documentBase = getDocumentBase();
1876 String withDocBase = resolveUrlForLocalOrAbsolute(path, documentBase);
1877 if (HttpUtils.isValidUrl(withDocBase))
1881 System.err.println("Prepended document base '" + documentBase
1882 + "' to make: '" + withDocBase + "'");
1884 protocol = DataSourceType.URL;
1889 * try relative to codebase (if different to document base)
1891 URL codeBase = getCodeBase();
1892 String withCodeBase = applet.resolveUrlForLocalOrAbsolute(path,
1894 if (!withCodeBase.equals(withDocBase)
1895 && HttpUtils.isValidUrl(withCodeBase))
1897 protocol = DataSourceType.URL;
1900 System.err.println("Prepended codebase '" + codeBase
1901 + "' to make: '" + withCodeBase + "'");
1903 return withCodeBase;
1907 * try locating by classloader; try this last so files in the directory
1908 * are resolved using document base
1910 if (inArchive(path))
1912 protocol = DataSourceType.CLASSLOADER;
1917 public LoadingThread(String file, String file2, JalviewLite _applet)
1920 this._file2 = file2;
1927 LoadJmolThread jmolchecker = new LoadJmolThread();
1928 jmolchecker.start();
1929 while (jmolchecker.notFinished())
1931 // wait around until the Jmol check is complete.
1935 } catch (Exception e)
1940 // applet.callInitCallback();
1944 * Load the alignment and any related files as specified by applet
1947 private void startLoading()
1949 dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");
1951 dbgMsg("Loading started.");
1953 AlignFrame newAlignFrame = readAlignment(_file);
1954 AlignFrame newAlignFrame2 = readAlignment(_file2);
1955 if (newAlignFrame != null)
1957 addToDisplay(newAlignFrame, newAlignFrame2);
1958 loadTree(newAlignFrame);
1960 loadScoreFile(newAlignFrame);
1962 loadFeatures(newAlignFrame);
1964 loadAnnotations(newAlignFrame);
1966 loadJnetFile(newAlignFrame);
1968 loadPdbFiles(newAlignFrame);
1973 applet.remove(launcher);
1980 * Add an AlignFrame to the display; or if two are provided, a SplitFrame.
1985 public void addToDisplay(AlignFrame af, AlignFrame af2)
1989 AlignmentI al1 = af.viewport.getAlignment();
1990 AlignmentI al2 = af2.viewport.getAlignment();
1991 AlignmentI cdna = al1.isNucleotide() ? al1 : al2;
1992 AlignmentI prot = al1.isNucleotide() ? al2 : al1;
1993 if (AlignmentUtils.mapProteinAlignmentToCdna(prot, cdna))
1996 SplitFrame sf = new SplitFrame(af, af2);
1997 sf.addToDisplay(embedded, JalviewLite.this);
2002 String msg = "Could not map any sequence in " + af2.getTitle()
2004 + (al1.isNucleotide() ? "protein product" : "cDNA")
2005 + " for " + af.getTitle();
2006 System.err.println(msg);
2010 af.addToDisplay(embedded);
2014 * Read the alignment file (from URL, text 'paste', or archive by
2019 protected AlignFrame readAlignment(String fileParam)
2021 if (fileParam == null)
2025 String resolvedFile = resolveFileProtocol(fileParam);
2026 AlignmentI al = null;
2029 FileFormatI format = new IdentifyFile().identify(resolvedFile,
2031 dbgMsg("File identified as '" + format + "'");
2032 al = new AppletFormatAdapter().readFile(resolvedFile, protocol,
2034 if ((al != null) && (al.getHeight() > 0))
2036 dbgMsg("Successfully loaded file.");
2037 al.setDataset(null);
2038 AlignFrame newAlignFrame = new AlignFrame(al, applet,
2039 resolvedFile, embedded, false);
2040 newAlignFrame.setTitle(resolvedFile);
2041 if (initialAlignFrame == null)
2043 initialAlignFrame = newAlignFrame;
2045 // update the focus.
2046 currentAlignFrame = newAlignFrame;
2048 if (protocol == DataSourceType.PASTE)
2050 newAlignFrame.setTitle(MessageManager.formatMessage(
2051 "label.sequences_from", new Object[] { applet
2052 .getDocumentBase().toString() }));
2055 newAlignFrame.statusBar.setText(MessageManager.formatMessage(
2056 "label.successfully_loaded_file",
2057 new Object[] { resolvedFile }));
2059 return newAlignFrame;
2061 } catch (java.io.IOException ex)
2063 dbgMsg("File load exception.");
2064 ex.printStackTrace();
2069 FileParse fp = new FileParse(resolvedFile, protocol);
2071 dbgMsg(">>>Dumping contents of '" + resolvedFile + "' " + "("
2073 while ((ln = fp.nextLine()) != null)
2077 dbgMsg(">>>Dump finished.");
2078 } catch (Exception e)
2081 .println("Exception when trying to dump the content of the file parameter.");
2082 e.printStackTrace();
2090 * Load PDBFiles if any specified by parameter(s). Returns true if loaded,
2096 protected boolean loadPdbFiles(AlignFrame alignFrame)
2098 boolean result = false;
2100 * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6 -
2101 * related to JAL-434
2104 applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",
2107 * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
2110 * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
2112 * <param name="PDBfile3" value="1q0o Q45135_9MICO">
2115 int pdbFileCount = 0;
2116 // Accumulate pdbs here if they are heading for the same view (if
2117 // alignPdbStructures is true)
2118 Vector pdbs = new Vector();
2119 // create a lazy matcher if we're asked to
2120 jalview.analysis.SequenceIdMatcher matcher = (applet
2121 .getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher(
2122 alignFrame.getAlignViewport().getAlignment()
2123 .getSequencesArray()) : null;
2128 if (pdbFileCount > 0)
2130 param = applet.getParameter("PDBFILE" + pdbFileCount);
2134 param = applet.getParameter("PDBFILE");
2139 PDBEntry pdb = new PDBEntry();
2142 SequenceI[] seqs = null;
2143 String[] chains = null;
2145 StringTokenizer st = new StringTokenizer(param, " ");
2147 if (st.countTokens() < 2)
2149 String sequence = applet.getParameter("PDBSEQ");
2150 if (sequence != null)
2152 seqs = new SequenceI[] { matcher == null ? (Sequence) alignFrame
2153 .getAlignViewport().getAlignment().findName(sequence)
2154 : matcher.findIdMatch(sequence) };
2160 param = st.nextToken();
2161 List<SequenceI> tmp = new ArrayList<SequenceI>();
2162 List<String> tmp2 = new ArrayList<String>();
2164 while (st.hasMoreTokens())
2166 seqstring = st.nextToken();
2167 StringTokenizer st2 = new StringTokenizer(seqstring, "=");
2168 if (st2.countTokens() > 1)
2170 // This is the chain
2171 tmp2.add(st2.nextToken());
2172 seqstring = st2.nextToken();
2174 tmp.add(matcher == null ? (Sequence) alignFrame
2175 .getAlignViewport().getAlignment()
2176 .findName(seqstring) : matcher.findIdMatch(seqstring));
2179 seqs = tmp.toArray(new SequenceI[tmp.size()]);
2180 if (tmp2.size() == tmp.size())
2182 chains = tmp2.toArray(new String[tmp2.size()]);
2185 param = resolveFileProtocol(param);
2186 // TODO check JAL-357 for files in a jar (CLASSLOADER)
2191 for (int i = 0; i < seqs.length; i++)
2193 if (seqs[i] != null)
2195 ((Sequence) seqs[i]).addPDBId(pdb);
2196 StructureSelectionManager.getStructureSelectionManager(
2197 applet).registerPDBEntry(pdb);
2201 if (JalviewLite.debug)
2203 // this may not really be a problem but we give a warning
2206 .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
2212 if (!alignPdbStructures)
2214 alignFrame.newStructureView(applet, pdb, seqs, chains,
2219 pdbs.addElement(new Object[] { pdb, seqs, chains, protocol });
2225 } while (param != null || pdbFileCount < 10);
2226 if (pdbs.size() > 0)
2228 SequenceI[][] seqs = new SequenceI[pdbs.size()][];
2229 PDBEntry[] pdb = new PDBEntry[pdbs.size()];
2230 String[][] chains = new String[pdbs.size()][];
2231 String[] protocols = new String[pdbs.size()];
2232 for (int pdbsi = 0, pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)
2234 Object[] o = (Object[]) pdbs.elementAt(pdbsi);
2235 pdb[pdbsi] = (PDBEntry) o[0];
2236 seqs[pdbsi] = (SequenceI[]) o[1];
2237 chains[pdbsi] = (String[]) o[2];
2238 protocols[pdbsi] = (String) o[3];
2240 alignFrame.alignedStructureView(applet, pdb, seqs, chains,
2248 * Load in a Jnetfile if specified by parameter. Returns true if loaded,
2254 protected boolean loadJnetFile(AlignFrame alignFrame)
2256 boolean result = false;
2257 String param = applet.getParameter("jnetfile");
2262 param = resolveFileProtocol(param);
2263 JPredFile predictions = new JPredFile(param, protocol);
2264 JnetAnnotationMaker.add_annotation(predictions,
2265 alignFrame.viewport.getAlignment(), 0, false);
2266 // false == do not add sequence profile from concise output
2267 SequenceI repseq = alignFrame.viewport.getAlignment()
2269 alignFrame.viewport.getAlignment().setSeqrep(repseq);
2270 ColumnSelection cs = new ColumnSelection();
2271 cs.hideInsertionsFor(repseq);
2272 alignFrame.viewport.setColumnSelection(cs);
2273 alignFrame.alignPanel.fontChanged();
2274 alignFrame.alignPanel.setScrollValues(0, 0);
2276 } catch (Exception ex)
2278 ex.printStackTrace();
2285 * Load annotations if specified by parameter. Returns true if loaded, else
2291 protected boolean loadAnnotations(AlignFrame alignFrame)
2293 boolean result = false;
2294 String param = applet.getParameter("annotations");
2297 param = resolveFileProtocol(param);
2299 if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
2302 alignFrame.alignPanel.fontChanged();
2303 alignFrame.alignPanel.setScrollValues(0, 0);
2309 .println("Annotations were not added from annotation file '"
2317 * Load features file and view settings as specified by parameters. Returns
2318 * true if features were loaded, else false.
2323 protected boolean loadFeatures(AlignFrame alignFrame)
2325 boolean result = false;
2326 // ///////////////////////////
2327 // modify display of features
2328 // we do this before any features have been loaded, ensuring any hidden
2329 // groups are hidden when features first displayed
2331 // hide specific groups
2333 String param = applet.getParameter("hidefeaturegroups");
2336 alignFrame.setFeatureGroupState(separatorListToArray(param), false);
2337 // applet.setFeatureGroupStateOn(newAlignFrame, param, false);
2339 // show specific groups
2340 param = applet.getParameter("showfeaturegroups");
2343 alignFrame.setFeatureGroupState(separatorListToArray(param), true);
2344 // applet.setFeatureGroupStateOn(newAlignFrame, param, true);
2346 // and now load features
2347 param = applet.getParameter("features");
2350 param = resolveFileProtocol(param);
2352 result = alignFrame.parseFeaturesFile(param, protocol);
2355 param = applet.getParameter("showFeatureSettings");
2356 if (param != null && param.equalsIgnoreCase(TRUE))
2358 alignFrame.viewport.setShowSequenceFeatures(true);
2359 new FeatureSettings(alignFrame.alignPanel);
2365 * Load a score file if specified by parameter. Returns true if file was
2366 * loaded, else false.
2370 protected boolean loadScoreFile(AlignFrame alignFrame)
2372 boolean result = false;
2373 String sScoreFile = applet.getParameter("scoreFile");
2374 if (sScoreFile != null && !"".equals(sScoreFile))
2381 .println("Attempting to load T-COFFEE score file from the scoreFile parameter");
2383 result = alignFrame.loadScoreFile(sScoreFile);
2387 .println("Failed to parse T-COFFEE parameter as a valid score file ('"
2388 + sScoreFile + "')");
2390 } catch (Exception e)
2392 System.err.printf("Cannot read score file: '%s'. Cause: %s \n",
2393 sScoreFile, e.getMessage());
2400 * Load a tree for the alignment if specified by parameter. Returns true if
2401 * a tree was loaded, else false.
2406 protected boolean loadTree(AlignFrame alignFrame)
2408 boolean result = false;
2409 String treeFile = applet.getParameter("tree");
2410 if (treeFile == null)
2412 treeFile = applet.getParameter("treeFile");
2415 if (treeFile != null)
2419 treeFile = resolveFileProtocol(treeFile);
2420 NewickFile fin = new NewickFile(treeFile, protocol);
2423 if (fin.getTree() != null)
2425 alignFrame.loadTree(fin, treeFile);
2427 dbgMsg("Successfully imported tree.");
2431 dbgMsg("Tree parameter did not resolve to a valid tree.");
2433 } catch (Exception ex)
2435 ex.printStackTrace();
2442 * Discovers whether the given file is in the Applet Archive
2448 boolean inArchive(String f)
2450 // This might throw a security exception in certain browsers
2451 // Netscape Communicator for instance.
2454 boolean rtn = (getClass().getResourceAsStream("/" + f) != null);
2457 System.err.println("Resource '" + f + "' was "
2458 + (rtn ? "" : "not ") + "located by classloader.");
2461 } catch (Exception ex)
2463 System.out.println("Exception checking resources: " + f + " " + ex);
2470 * @return the default alignFrame acted on by the public applet methods. May
2471 * return null with an error message on System.err indicating the
2474 public AlignFrame getDefaultTargetFrame()
2476 if (currentAlignFrame != null)
2478 return currentAlignFrame;
2480 if (initialAlignFrame != null)
2482 return initialAlignFrame;
2485 .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
2490 * separator used for separatorList
2492 protected String separator = "" + ((char) 0x00AC); // the default used to be
2493 // '|' but many sequence
2494 // IDS include pipes.
2497 * set to enable the URL based javascript execution mechanism
2499 public boolean jsfallbackEnabled = false;
2502 * parse the string into a list
2505 * @return elements separated by separator
2507 public String[] separatorListToArray(String list)
2509 return separatorListToArray(list, separator);
2513 * parse the string into a list
2517 * @return elements separated by separator
2519 public static String[] separatorListToArray(String list, String separator)
2521 // TODO use StringUtils version (slightly different...)
2522 int seplen = separator.length();
2523 if (list == null || list.equals("") || list.equals(separator))
2527 java.util.Vector jv = new Vector();
2529 while ((pos = list.indexOf(separator, cp)) > cp)
2531 jv.addElement(list.substring(cp, pos));
2534 if (cp < list.length())
2536 String c = list.substring(cp);
2537 if (!c.equals(separator))
2544 String[] v = new String[jv.size()];
2545 for (int i = 0; i < v.length; i++)
2547 v[i] = (String) jv.elementAt(i);
2549 jv.removeAllElements();
2552 System.err.println("Array from '" + separator
2553 + "' separated List:\n" + v.length);
2554 for (int i = 0; i < v.length; i++)
2556 System.err.println("item " + i + " '" + v[i] + "'");
2563 System.err.println("Empty Array from '" + separator
2564 + "' separated List");
2570 * concatenate the list with separator
2573 * @return concatenated string
2575 public String arrayToSeparatorList(String[] list)
2577 return arrayToSeparatorList(list, separator);
2581 * concatenate the list with separator
2585 * @return concatenated string
2587 public static String arrayToSeparatorList(String[] list, String separator)
2589 // TODO use StringUtils version
2590 StringBuffer v = new StringBuffer();
2591 if (list != null && list.length > 0)
2593 for (int i = 0, iSize = list.length; i < iSize; i++)
2595 if (list[i] != null)
2599 v.append(separator);
2606 System.err.println("Returning '" + separator
2607 + "' separated List:\n");
2608 System.err.println(v);
2610 return v.toString();
2614 System.err.println("Returning empty '" + separator
2615 + "' separated List\n");
2617 return "" + separator;
2623 * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
2626 public String getFeatureGroups()
2628 String lst = arrayToSeparatorList(getDefaultTargetFrame()
2629 .getFeatureGroups());
2637 * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame
2641 public String getFeatureGroupsOn(AlignFrame alf)
2643 String lst = arrayToSeparatorList(alf.getFeatureGroups());
2650 * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)
2653 public String getFeatureGroupsOfState(boolean visible)
2655 return arrayToSeparatorList(getDefaultTargetFrame()
2656 .getFeatureGroupsOfState(visible));
2663 * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui
2664 * .AlignFrame, boolean)
2667 public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
2669 return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
2675 * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui.
2676 * AlignFrame, java.lang.String, boolean)
2679 public void setFeatureGroupStateOn(final AlignFrame alf,
2680 final String groups, boolean state)
2682 final boolean st = state;// !(state==null || state.equals("") ||
2683 // state.toLowerCase().equals("false"));
2684 java.awt.EventQueue.invokeLater(new Runnable()
2689 alf.setFeatureGroupState(separatorListToArray(groups), st);
2697 * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupState(java.lang.String,
2701 public void setFeatureGroupState(String groups, boolean state)
2703 setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
2709 * @see jalview.bin.JalviewLiteJsApi#getSeparator()
2712 public String getSeparator()
2720 * @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String)
2723 public void setSeparator(String separator)
2725 if (separator == null || separator.length() < 1)
2728 separator = "" + ((char) 0x00AC);
2730 this.separator = separator;
2733 System.err.println("Default Separator now: '" + separator + "'");
2738 * get boolean value of applet parameter 'name' and return default if
2739 * parameter is not set
2744 * the value to return otherwise
2745 * @return true or false
2747 public boolean getDefaultParameter(String name, boolean def)
2750 if ((stn = getParameter(name)) == null)
2754 if (TRUE.equalsIgnoreCase(stn))
2764 * @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame,
2765 * java.lang.String, java.lang.String, java.lang.String)
2768 public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
2769 String pdbEntryString, String pdbFile)
2771 return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);
2774 protected void setAlignPdbStructures(boolean alignPdbStructures)
2776 this.alignPdbStructures = alignPdbStructures;
2779 public boolean isAlignPdbStructures()
2781 return alignPdbStructures;
2787 // callInitCallback();
2790 private Hashtable<String, long[]> jshashes = new Hashtable<String, long[]>();
2792 private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<String, Hashtable<String, String[]>>();
2794 public void setJsMessageSet(String messageclass, String viewId,
2795 String[] colcommands)
2797 Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
2800 msgset = new Hashtable<String, String[]>();
2801 jsmessages.put(messageclass, msgset);
2803 msgset.put(viewId, colcommands);
2804 long[] l = new long[colcommands.length];
2805 for (int i = 0; i < colcommands.length; i++)
2807 l[i] = colcommands[i].hashCode();
2809 jshashes.put(messageclass + "|" + viewId, l);
2815 * @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String,
2819 public String getJsMessage(String messageclass, String viewId)
2821 Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
2824 String[] msgs = msgset.get(viewId);
2827 for (int i = 0; i < msgs.length; i++)
2829 if (msgs[i] != null)
2841 public boolean isJsMessageSetChanged(String string, String string2,
2842 String[] colcommands)
2844 long[] l = jshashes.get(string + "|" + string2);
2845 if (l == null && colcommands != null)
2849 for (int i = 0; i < colcommands.length; i++)
2851 if (l[i] != colcommands[i].hashCode())
2859 private Vector jsExecQueue = new Vector();
2861 public Vector getJsExecQueue()
2866 public void setExecutor(JSFunctionExec jsFunctionExec2)
2868 jsFunctionExec = jsFunctionExec2;
2872 * return the given colour value parameter or the given default if parameter
2879 public Color getDefaultColourParameter(String colparam, Color defcolour)
2881 String colprop = getParameter(colparam);
2882 if (colprop == null || colprop.trim().length() == 0)
2886 Color col = jalview.schemes.ColourSchemeProperty
2887 .getAWTColorFromName(colprop);
2892 col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
2893 } catch (Exception ex)
2895 System.err.println("Couldn't parse '" + colprop
2896 + "' as a colour for " + colparam);
2900 return (col == null) ? defcolour : col;
2904 public void openJalviewHelpUrl()
2906 String helpUrl = getParameter("jalviewhelpurl");
2907 if (helpUrl == null || helpUrl.trim().length() < 5)
2909 helpUrl = "http://www.jalview.org/help.html";
2911 showURL(helpUrl, "HELP");
2915 * form a complete URL given a path to a resource and a reference location on
2919 * - an absolute path on the same server as localref or a document
2920 * located relative to localref
2922 * - a URL on the same server as url
2923 * @return a complete URL for the resource located by url
2925 private String resolveUrlForLocalOrAbsolute(String targetPath,
2928 String resolvedPath = "";
2929 if (targetPath.startsWith("/"))
2931 String codebase = localref.toString();
2932 String localfile = localref.getFile();
2933 resolvedPath = codebase.substring(0,
2934 codebase.length() - localfile.length())
2936 return resolvedPath;
2940 * get URL path and strip off any trailing file e.g.
2941 * www.jalview.org/examples/index.html#applets?a=b is trimmed to
2942 * www.jalview.org/examples/
2944 String urlPath = localref.toString();
2945 String directoryPath = urlPath;
2946 int lastSeparator = directoryPath.lastIndexOf("/");
2947 if (lastSeparator > 0)
2949 directoryPath = directoryPath.substring(0, lastSeparator + 1);
2952 if (targetPath.startsWith("/"))
2955 * construct absolute URL to a file on the server - this is not allowed?
2957 // String localfile = localref.getFile();
2958 // resolvedPath = urlPath.substring(0,
2959 // urlPath.length() - localfile.length())
2961 resolvedPath = directoryPath + targetPath.substring(1);
2965 resolvedPath = directoryPath + targetPath;
2969 System.err.println("resolveUrlForLocalOrAbsolute returning "
2972 return resolvedPath;
2976 * open a URL in the browser - resolving it according to relative refs and
2977 * coping with javascript: protocol if necessary.
2982 public void showURL(String url, String target)
2986 if (url.indexOf(":") == -1)
2988 // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
2990 // Should really use docbase, not codebase.
2992 url = resolveUrlForLocalOrAbsolute(
2994 prepend = getDefaultParameter("resolvetocodebase", false) ? getCodeBase()
2995 : getDocumentBase());
2999 .println("Show url (prepended "
3001 + " - toggle resolvetocodebase if code/docbase resolution is wrong): "
3009 System.err.println("Show url: " + url);
3012 if (url.indexOf("javascript:") == 0)
3014 // no target for the javascript context
3015 getAppletContext().showDocument(new java.net.URL(url));
3019 getAppletContext().showDocument(new java.net.URL(url), target);
3021 } catch (Exception ex)
3023 ex.printStackTrace();
3028 * bind structures in a viewer to any matching sequences in an alignFrame (use
3029 * sequenceIds to limit scope of search to specific sequences)
3033 * @param sequenceIds
3034 * @return TODO: consider making an exception structure for indicating when
3035 * binding fails public SequenceStructureBinding
3036 * addStructureViewInstance( AlignFrame alFrame, Object viewer, String
3039 * if (sequenceIds != null && sequenceIds.length() > 0) { return
3040 * alFrame.addStructureViewInstance(viewer,
3041 * separatorListToArray(sequenceIds)); } else { return
3042 * alFrame.addStructureViewInstance(viewer, null); } // return null; }