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.api.StructureSelectionManagerProvider;
24 import jalview.appletgui.AlignFrame;
25 import jalview.appletgui.AlignViewport;
26 import jalview.appletgui.EmbmenuFrame;
27 import jalview.appletgui.FeatureSettings;
28 import jalview.appletgui.SplitFrame;
29 import jalview.datamodel.Alignment;
30 import jalview.datamodel.AlignmentI;
31 import jalview.datamodel.AlignmentOrder;
32 import jalview.datamodel.ColumnSelection;
33 import jalview.datamodel.PDBEntry;
34 import jalview.datamodel.Sequence;
35 import jalview.datamodel.SequenceGroup;
36 import jalview.datamodel.SequenceI;
37 import jalview.io.AnnotationFile;
38 import jalview.io.AppletFormatAdapter;
39 import jalview.io.FileParse;
40 import jalview.io.IdentifyFile;
41 import jalview.io.JPredFile;
42 import jalview.io.JnetAnnotationMaker;
43 import jalview.io.NewickFile;
44 import jalview.javascript.JSFunctionExec;
45 import jalview.javascript.JalviewLiteJsApi;
46 import jalview.javascript.JsCallBack;
47 import jalview.structure.SelectionListener;
48 import jalview.structure.StructureSelectionManager;
49 import jalview.util.MessageManager;
51 import java.applet.Applet;
52 import java.awt.Button;
53 import java.awt.Color;
54 import java.awt.Component;
55 import java.awt.EventQueue;
57 import java.awt.Frame;
58 import java.awt.Graphics;
59 import java.awt.event.ActionEvent;
60 import java.awt.event.WindowAdapter;
61 import java.awt.event.WindowEvent;
62 import java.io.BufferedReader;
63 import java.io.IOException;
64 import java.io.InputStream;
65 import java.io.InputStreamReader;
67 import java.util.Hashtable;
68 import java.util.List;
69 import java.util.StringTokenizer;
70 import java.util.Vector;
72 import netscape.javascript.JSException;
73 import netscape.javascript.JSObject;
76 * Jalview Applet. Runs in Java 1.18 runtime
79 * @version $Revision: 1.92 $
81 public class JalviewLite extends Applet implements
82 StructureSelectionManagerProvider, JalviewLiteJsApi
85 private static final String TRUE = "true";
87 private static final String FALSE = "false";
89 public StructureSelectionManager getStructureSelectionManager()
91 return StructureSelectionManager.getStructureSelectionManager(this);
94 // /////////////////////////////////////////
95 // The following public methods maybe called
96 // externally, eg via javascript in HTML page
100 * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences()
102 public String getSelectedSequences()
104 return getSelectedSequencesFrom(getDefaultTargetFrame());
110 * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
112 public String getSelectedSequences(String sep)
114 return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);
121 * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
124 public String getSelectedSequencesFrom(AlignFrame alf)
126 return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);
133 * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
134 * .AlignFrame, java.lang.String)
136 public String getSelectedSequencesFrom(AlignFrame alf, String sep)
138 StringBuffer result = new StringBuffer("");
139 if (sep == null || sep.length() == 0)
141 sep = separator; // "+0x00AC;
143 if (alf.viewport.getSelectionGroup() != null)
145 SequenceI[] seqs = alf.viewport.getSelectionGroup()
146 .getSequencesInOrder(alf.viewport.getAlignment());
148 for (int i = 0; i < seqs.length; i++)
150 result.append(seqs[i].getName());
155 return result.toString();
161 * @see jalview.bin.JalviewLiteJsApi#highlight(java.lang.String,
162 * java.lang.String, java.lang.String)
164 public void highlight(String sequenceId, String position,
165 String alignedPosition)
167 highlightIn(getDefaultTargetFrame(), sequenceId, position,
174 * @see jalview.bin.JalviewLiteJsApi#highlightIn(jalview.appletgui.AlignFrame,
175 * java.lang.String, java.lang.String, java.lang.String)
177 public void highlightIn(final AlignFrame alf, final String sequenceId,
178 final String position, final String alignedPosition)
180 // TODO: could try to highlight in all alignments if alf==null
181 jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
182 alf.viewport.getAlignment().getSequencesArray());
183 final SequenceI sq = matcher.findIdMatch(sequenceId);
189 apos = new Integer(position).intValue();
191 } catch (NumberFormatException ex)
195 final StructureSelectionManagerProvider me = this;
196 final int pos = apos;
197 // use vamsas listener to broadcast to all listeners in scope
198 if (alignedPosition != null
199 && (alignedPosition.trim().length() == 0 || alignedPosition
200 .toLowerCase().indexOf("false") > -1))
202 java.awt.EventQueue.invokeLater(new Runnable()
207 StructureSelectionManager.getStructureSelectionManager(me)
208 .mouseOverVamsasSequence(sq, sq.findIndex(pos), null);
214 java.awt.EventQueue.invokeLater(new Runnable()
219 StructureSelectionManager.getStructureSelectionManager(me)
220 .mouseOverVamsasSequence(sq, pos, null);
230 * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
233 public void select(String sequenceIds, String columns)
235 selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator);
241 * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
242 * java.lang.String, java.lang.String)
244 public void select(String sequenceIds, String columns, String sep)
246 selectIn(getDefaultTargetFrame(), sequenceIds, columns, sep);
252 * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
253 * java.lang.String, java.lang.String)
255 public void selectIn(AlignFrame alf, String sequenceIds, String columns)
257 selectIn(alf, sequenceIds, columns, separator);
263 * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
264 * java.lang.String, java.lang.String, java.lang.String)
266 public void selectIn(final AlignFrame alf, String sequenceIds,
267 String columns, String sep)
269 if (sep == null || sep.length() == 0)
277 System.err.println("Selecting region using separator string '"
282 String[] ids = separatorListToArray(sequenceIds, sep);
283 String[] cols = separatorListToArray(columns, sep);
284 final SequenceGroup sel = new SequenceGroup();
285 final ColumnSelection csel = new ColumnSelection();
286 AlignmentI al = alf.viewport.getAlignment();
287 jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
288 alf.viewport.getAlignment().getSequencesArray());
289 int start = 0, end = al.getWidth(), alw = al.getWidth();
290 boolean seqsfound = true;
291 if (ids != null && ids.length > 0)
294 for (int i = 0; i < ids.length; i++)
296 if (ids[i].trim().length() == 0)
300 SequenceI sq = matcher.findIdMatch(ids[i]);
304 sel.addSequence(sq, false);
308 boolean inseqpos = false;
309 if (cols != null && cols.length > 0)
311 boolean seset = false;
312 for (int i = 0; i < cols.length; i++)
314 String cl = cols[i].trim();
315 if (cl.length() == 0)
320 if ((p = cl.indexOf("-")) > -1)
322 int from = -1, to = -1;
325 from = new Integer(cl.substring(0, p)).intValue();
327 } catch (NumberFormatException ex)
330 .println("ERROR: Couldn't parse first integer in range element column selection string '"
331 + cl + "' - format is 'from-to'");
336 to = new Integer(cl.substring(p + 1)).intValue();
338 } catch (NumberFormatException ex)
341 .println("ERROR: Couldn't parse second integer in range element column selection string '"
342 + cl + "' - format is 'from-to'");
345 if (from >= 0 && to >= 0)
362 // comment to prevent range extension
372 for (int r = from; r <= to; r++)
374 if (r >= 0 && r < alw)
381 System.err.println("Range '" + cl + "' deparsed as [" + from
387 System.err.println("ERROR: Invalid Range '" + cl
388 + "' deparsed as [" + from + "," + to + "]");
396 r = new Integer(cl).intValue();
398 } catch (NumberFormatException ex)
400 if (cl.toLowerCase().equals("sequence"))
402 // we are in the dataset sequence's coordinate frame.
408 .println("ERROR: Couldn't parse integer from point selection element of column selection string '"
413 if (r >= 0 && r <= alw)
423 // comment to prevent range extension
436 System.err.println("Point selection '" + cl
437 + "' deparsed as [" + r + "]");
442 System.err.println("ERROR: Invalid Point selection '" + cl
443 + "' deparsed as [" + r + "]");
450 // we only propagate the selection when it was the null selection, or the
451 // given sequences were found in the alignment.
452 if (inseqpos && sel.getSize() > 0)
454 // assume first sequence provides reference frame ?
455 SequenceI rs = sel.getSequenceAt(0);
456 start = rs.findIndex(start);
457 end = rs.findIndex(end);
460 List<Integer> cs = csel.getSelected();
462 for (Integer selectedCol : cs)
464 csel.addElement(rs.findIndex(selectedCol));
468 sel.setStartRes(start);
470 EventQueue.invokeLater(new Runnable()
475 alf.select(sel, csel);
485 * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignment(java.lang.
486 * String, java.lang.String)
488 public String getSelectedSequencesAsAlignment(String format, String suffix)
490 return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(),
498 * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignmentFrom(jalview
499 * .appletgui.AlignFrame, java.lang.String, java.lang.String)
501 public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
502 String format, String suffix)
506 boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
507 if (alf.viewport.getSelectionGroup() != null)
509 // JBPNote: getSelectionAsNewSequence behaviour has changed - this
510 // method now returns a full copy of sequence data
511 // TODO consider using getSequenceSelection instead here
512 String reply = new AppletFormatAdapter().formatSequences(format,
513 new Alignment(alf.viewport.getSelectionAsNewSequence()),
517 } catch (Exception ex)
519 ex.printStackTrace();
520 return "Error retrieving alignment in " + format + " format. ";
528 * @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder()
530 public String getAlignmentOrder()
532 return getAlignmentOrderFrom(getDefaultTargetFrame());
539 * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
542 public String getAlignmentOrderFrom(AlignFrame alf)
544 return getAlignmentOrderFrom(alf, separator);
551 * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
552 * , java.lang.String)
554 public String getAlignmentOrderFrom(AlignFrame alf, String sep)
556 AlignmentI alorder = alf.getAlignViewport().getAlignment();
557 String[] order = new String[alorder.getHeight()];
558 for (int i = 0; i < order.length; i++)
560 order[i] = alorder.getSequenceAt(i).getName();
562 return arrayToSeparatorList(order);
568 * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
571 public String orderBy(String order, String undoName)
573 return orderBy(order, undoName, separator);
579 * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
580 * java.lang.String, java.lang.String)
582 public String orderBy(String order, String undoName, String sep)
584 return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep);
591 * jalview.bin.JalviewLiteJsApi#orderAlignmentBy(jalview.appletgui.AlignFrame,
592 * java.lang.String, java.lang.String, java.lang.String)
594 public String orderAlignmentBy(AlignFrame alf, String order,
595 String undoName, String sep)
597 String[] ids = separatorListToArray(order, sep);
598 SequenceI[] sqs = null;
599 if (ids != null && ids.length > 0)
601 jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
602 alf.viewport.getAlignment().getSequencesArray());
604 sqs = new SequenceI[ids.length];
605 for (int i = 0; i < ids.length; i++)
607 if (ids[i].trim().length() == 0)
611 SequenceI sq = matcher.findIdMatch(ids[i]);
619 SequenceI[] sqq = new SequenceI[s];
620 System.arraycopy(sqs, 0, sqq, 0, s);
633 final AlignmentOrder aorder = new AlignmentOrder(sqs);
635 if (undoName != null && undoName.trim().length() == 0)
639 final String _undoName = undoName;
640 // TODO: deal with synchronization here: cannot raise any events until after
641 // this has returned.
642 return alf.sortBy(aorder, _undoName) ? TRUE : "";
648 * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String)
650 public String getAlignment(String format)
652 return getAlignmentFrom(getDefaultTargetFrame(), format, TRUE);
659 * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
662 public String getAlignmentFrom(AlignFrame alf, String format)
664 return getAlignmentFrom(alf, format, TRUE);
670 * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String,
673 public String getAlignment(String format, String suffix)
675 return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);
682 * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
683 * java.lang.String, java.lang.String)
685 public String getAlignmentFrom(AlignFrame alf, String format,
690 boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
692 String reply = new AppletFormatAdapter().formatSequences(format,
693 alf.viewport.getAlignment(), seqlimits);
695 } catch (Exception ex)
697 ex.printStackTrace();
698 return "Error retrieving alignment in " + format + " format. ";
705 * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
707 public void loadAnnotation(String annotation)
709 loadAnnotationFrom(getDefaultTargetFrame(), annotation);
716 * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
717 * , java.lang.String)
719 public void loadAnnotationFrom(AlignFrame alf, String annotation)
721 if (new AnnotationFile().annotateAlignmentView(alf.getAlignViewport(),
722 annotation, AppletFormatAdapter.PASTE))
724 alf.alignPanel.fontChanged();
725 alf.alignPanel.setScrollValues(0, 0);
729 alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
736 * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
738 public void loadFeatures(String features, boolean autoenabledisplay)
740 loadFeaturesFrom(getDefaultTargetFrame(), features, autoenabledisplay);
747 * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
748 * , java.lang.String)
750 public boolean loadFeaturesFrom(AlignFrame alf, String features,
751 boolean autoenabledisplay)
753 return alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE,
760 * @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String)
762 public String getFeatures(String format)
764 return getFeaturesFrom(getDefaultTargetFrame(), format);
771 * jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame,
774 public String getFeaturesFrom(AlignFrame alf, String format)
776 return alf.outputFeatures(false, format);
782 * @see jalview.bin.JalviewLiteJsApi#getAnnotation()
784 public String getAnnotation()
786 return getAnnotationFrom(getDefaultTargetFrame());
793 * jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame
796 public String getAnnotationFrom(AlignFrame alf)
798 return alf.outputAnnotations(false);
804 * @see jalview.bin.JalviewLiteJsApi#newView()
806 public AlignFrame newView()
808 return newViewFrom(getDefaultTargetFrame());
814 * @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String)
816 public AlignFrame newView(String name)
818 return newViewFrom(getDefaultTargetFrame(), name);
824 * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame)
826 public AlignFrame newViewFrom(AlignFrame alf)
828 return alf.newView(null);
834 * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame,
837 public AlignFrame newViewFrom(AlignFrame alf, String name)
839 return alf.newView(name);
845 * @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String,
848 public AlignFrame loadAlignment(String text, String title)
852 String format = new IdentifyFile().Identify(text,
853 AppletFormatAdapter.PASTE);
856 al = new AppletFormatAdapter().readFile(text,
857 AppletFormatAdapter.PASTE, format);
858 if (al.getHeight() > 0)
860 return new AlignFrame(al, this, title, false);
862 } catch (java.io.IOException ex)
864 ex.printStackTrace();
872 * @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String)
874 public void setMouseoverListener(String listener)
876 setMouseoverListener(currentAlignFrame, listener);
879 private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<jalview.javascript.JSFunctionExec>();
885 * jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame
886 * , java.lang.String)
888 public void setMouseoverListener(AlignFrame af, String listener)
890 if (listener != null)
892 listener = listener.trim();
893 if (listener.length() == 0)
896 .println("jalview Javascript error: Ignoring empty function for mouseover listener.");
900 jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener(
902 javascriptListeners.addElement(mol);
903 StructureSelectionManager.getStructureSelectionManager(this)
904 .addStructureViewerListener(mol);
907 System.err.println("Added a mouseover listener for "
908 + ((af == null) ? "All frames" : "Just views for "
909 + af.getAlignViewport().getSequenceSetId()));
910 System.err.println("There are now " + javascriptListeners.size()
911 + " listeners in total.");
918 * @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String)
920 public void setSelectionListener(String listener)
922 setSelectionListener(null, listener);
929 * jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame
930 * , java.lang.String)
932 public void setSelectionListener(AlignFrame af, String listener)
934 if (listener != null)
936 listener = listener.trim();
937 if (listener.length() == 0)
940 .println("jalview Javascript error: Ignoring empty function for selection listener.");
944 jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender(
946 javascriptListeners.addElement(mol);
947 StructureSelectionManager.getStructureSelectionManager(this)
948 .addSelectionListener(mol);
951 System.err.println("Added a selection listener for "
952 + ((af == null) ? "All frames" : "Just views for "
953 + af.getAlignViewport().getSequenceSetId()));
954 System.err.println("There are now " + javascriptListeners.size()
955 + " listeners in total.");
962 * @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String,
965 public void setStructureListener(String listener, String modelSet)
967 if (listener != null)
969 listener = listener.trim();
970 if (listener.length() == 0)
973 .println("jalview Javascript error: Ignoring empty function for selection listener.");
977 jalview.javascript.MouseOverStructureListener mol = new jalview.javascript.MouseOverStructureListener(
978 this, listener, separatorListToArray(modelSet));
979 javascriptListeners.addElement(mol);
980 StructureSelectionManager.getStructureSelectionManager(this)
981 .addStructureViewerListener(mol);
984 System.err.println("Added a javascript structure viewer listener '"
986 System.err.println("There are now " + javascriptListeners.size()
987 + " listeners in total.");
995 * jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui
996 * .AlignFrame, java.lang.String)
998 public void removeJavascriptListener(AlignFrame af, String listener)
1000 if (listener != null)
1002 listener = listener.trim();
1003 if (listener.length() == 0)
1008 boolean rprt = false;
1009 for (int ms = 0, msSize = javascriptListeners.size(); ms < msSize;)
1011 Object lstn = javascriptListeners.elementAt(ms);
1012 JsCallBack lstner = (JsCallBack) lstn;
1013 if ((af == null || lstner.getAlignFrame() == af)
1014 && (listener == null || lstner.getListenerFunction().equals(
1017 javascriptListeners.removeElement(lstner);
1019 if (lstner instanceof SelectionListener)
1021 StructureSelectionManager.getStructureSelectionManager(this)
1022 .removeSelectionListener((SelectionListener) lstner);
1026 StructureSelectionManager.getStructureSelectionManager(this)
1027 .removeStructureViewerListener(lstner, null);
1032 System.err.println("Removed listener '" + listener + "'");
1042 System.err.println("There are now " + javascriptListeners.size()
1043 + " listeners in total.");
1049 System.err.println("Applet " + getName() + " stop().");
1053 public void destroy()
1055 System.err.println("Applet " + getName() + " destroy().");
1059 private void tidyUp()
1062 if (currentAlignFrame != null && currentAlignFrame.viewport != null
1063 && currentAlignFrame.viewport.applet != null)
1065 AlignViewport av = currentAlignFrame.viewport;
1066 currentAlignFrame.closeMenuItem_actionPerformed();
1068 currentAlignFrame = null;
1070 if (javascriptListeners != null)
1072 while (javascriptListeners.size() > 0)
1074 jalview.javascript.JSFunctionExec mol = javascriptListeners
1076 javascriptListeners.removeElement(mol);
1077 if (mol instanceof SelectionListener)
1079 StructureSelectionManager.getStructureSelectionManager(this)
1080 .removeSelectionListener((SelectionListener) mol);
1084 StructureSelectionManager.getStructureSelectionManager(this)
1085 .removeStructureViewerListener(mol, null);
1090 if (jsFunctionExec != null)
1092 jsFunctionExec.stopQueue();
1093 jsFunctionExec.jvlite = null;
1095 initialAlignFrame = null;
1096 jsFunctionExec = null;
1097 javascriptListeners = null;
1098 StructureSelectionManager.release(this);
1101 private jalview.javascript.JSFunctionExec jsFunctionExec;
1106 * @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String,
1107 * java.lang.String, java.lang.String)
1109 public void mouseOverStructure(final String pdbResNum,
1110 final String chain, final String pdbfile)
1112 final StructureSelectionManagerProvider me = this;
1113 java.awt.EventQueue.invokeLater(new Runnable()
1120 StructureSelectionManager.getStructureSelectionManager(me)
1121 .mouseOverStructure(new Integer(pdbResNum).intValue(),
1125 System.err.println("mouseOver for '" + pdbResNum
1126 + "' in chain '" + chain + "' in structure '" + pdbfile
1129 } catch (NumberFormatException e)
1131 System.err.println("Ignoring invalid residue number string '"
1143 * jalview.bin.JalviewLiteJsApi#scrollViewToIn(jalview.appletgui.AlignFrame,
1144 * java.lang.String, java.lang.String)
1146 public void scrollViewToIn(final AlignFrame alf, final String topRow,
1147 final String leftHandColumn)
1149 java.awt.EventQueue.invokeLater(new Runnable()
1156 alf.scrollTo(new Integer(topRow).intValue(), new Integer(
1157 leftHandColumn).intValue());
1159 } catch (Exception ex)
1161 System.err.println("Couldn't parse integer arguments (topRow='"
1162 + topRow + "' and leftHandColumn='" + leftHandColumn
1164 ex.printStackTrace();
1174 * jalview.javascript.JalviewLiteJsApi#scrollViewToRowIn(jalview.appletgui
1175 * .AlignFrame, java.lang.String)
1178 public void scrollViewToRowIn(final AlignFrame alf, final String topRow)
1181 java.awt.EventQueue.invokeLater(new Runnable()
1188 alf.scrollToRow(new Integer(topRow).intValue());
1190 } catch (Exception ex)
1192 System.err.println("Couldn't parse integer arguments (topRow='"
1194 ex.printStackTrace();
1205 * jalview.javascript.JalviewLiteJsApi#scrollViewToColumnIn(jalview.appletgui
1206 * .AlignFrame, java.lang.String)
1209 public void scrollViewToColumnIn(final AlignFrame alf,
1210 final String leftHandColumn)
1212 java.awt.EventQueue.invokeLater(new Runnable()
1220 alf.scrollToColumn(new Integer(leftHandColumn).intValue());
1222 } catch (Exception ex)
1225 .println("Couldn't parse integer arguments (leftHandColumn='"
1226 + leftHandColumn + "')");
1227 ex.printStackTrace();
1234 // //////////////////////////////////////////////
1235 // //////////////////////////////////////////////
1237 public static int lastFrameX = 200;
1239 public static int lastFrameY = 200;
1241 boolean fileFound = true;
1243 String file = "No file";
1245 String file2 = "No file";
1247 Button launcher = new Button(
1248 MessageManager.getString("label.start_jalview"));
1251 * The currentAlignFrame is static, it will change if and when the user
1252 * selects a new window. Note that it will *never* point back to the embedded
1253 * AlignFrame if the applet is started as embedded on the page and then
1254 * afterwards a new view is created.
1256 public AlignFrame currentAlignFrame = null;
1259 * This is the first frame to be displayed, and does not change. API calls
1260 * will default to this instance if currentAlignFrame is null.
1262 AlignFrame initialAlignFrame = null;
1264 boolean embedded = false;
1266 private boolean checkForJmol = true;
1268 private boolean checkedForJmol = false; // ensure we don't check for jmol
1270 // every time the app is re-inited
1272 public boolean jmolAvailable = false;
1274 private boolean alignPdbStructures = false;
1277 * use an external structure viewer exclusively (no jmols or MCViews will be
1278 * opened by JalviewLite itself)
1280 public boolean useXtrnalSviewer = false;
1282 public static boolean debug = false;
1284 static String builddate = null, version = null, installation = null;
1286 private static void initBuildDetails()
1288 if (builddate == null)
1290 builddate = "unknown";
1292 installation = "Webstart";
1293 java.net.URL url = JalviewLite.class
1294 .getResource("/.build_properties");
1299 BufferedReader reader = new BufferedReader(new InputStreamReader(
1302 while ((line = reader.readLine()) != null)
1304 if (line.indexOf("VERSION") > -1)
1306 version = line.substring(line.indexOf("=") + 1);
1308 if (line.indexOf("BUILD_DATE") > -1)
1310 builddate = line.substring(line.indexOf("=") + 1);
1312 if (line.indexOf("INSTALLATION") > -1)
1314 installation = line.substring(line.indexOf("=") + 1);
1317 } catch (Exception ex)
1319 ex.printStackTrace();
1325 public static String getBuildDate()
1331 public static String getInstallation()
1334 return installation;
1337 public static String getVersion()
1343 // public JSObject scriptObject = null;
1346 * init method for Jalview Applet
1350 // remove any handlers that might be hanging around from an earlier instance
1355 System.err.println("Applet context is '"
1356 + getAppletContext().getClass().toString() + "'");
1358 JSObject scriptObject = JSObject.getWindow(this);
1359 if (debug && scriptObject != null)
1361 System.err.println("Applet has Javascript callback support.");
1364 } catch (Exception ex)
1367 .println("Warning: No JalviewLite javascript callbacks available.");
1370 ex.printStackTrace();
1374 * turn on extra applet debugging
1376 debug = TRUE.equalsIgnoreCase(getParameter("debug"));
1380 System.err.println("JalviewLite Version " + getVersion());
1381 System.err.println("Build Date : " + getBuildDate());
1382 System.err.println("Installation : " + getInstallation());
1385 String externalsviewer = getParameter("externalstructureviewer");
1386 if (externalsviewer != null)
1388 useXtrnalSviewer = externalsviewer.trim().toLowerCase()
1392 * if true disable the check for jmol
1394 String chkforJmol = getParameter("nojmol");
1395 if (chkforJmol != null)
1397 checkForJmol = !chkforJmol.equals(TRUE);
1400 * get the separator parameter if present
1402 String sep = getParameter("separator");
1405 if (sep.length() > 0)
1410 System.err.println("Separator set to '" + separator + "'");
1415 throw new Error(MessageManager.getString("error.invalid_separator_parameter"));
1421 String param = getParameter("RGB");
1427 r = Integer.parseInt(param.substring(0, 2), 16);
1428 g = Integer.parseInt(param.substring(2, 4), 16);
1429 b = Integer.parseInt(param.substring(4, 6), 16);
1430 } catch (Exception ex)
1437 param = getParameter("label");
1440 launcher.setLabel(param);
1443 setBackground(new Color(r, g, b));
1445 file = getParameter("file");
1449 // Maybe the sequences are added as parameters
1450 StringBuffer data = new StringBuffer("PASTE");
1452 while ((file = getParameter("sequence" + i)) != null)
1454 data.append(file.toString() + "\n");
1457 if (data.length() > 5)
1459 file = data.toString();
1462 file2 = getParameter("file2");
1464 embedded = TRUE.equalsIgnoreCase(getParameter("embedded"));
1467 LoadingThread loader = new LoadingThread(file, file2, this);
1470 else if (file != null)
1473 * Start the applet immediately or show a button to start it
1475 if (FALSE.equalsIgnoreCase(getParameter("showbutton")))
1477 LoadingThread loader = new LoadingThread(file, file2, this);
1483 launcher.addActionListener(new java.awt.event.ActionListener()
1485 public void actionPerformed(ActionEvent e)
1487 LoadingThread loader = new LoadingThread(file, file2,
1496 // jalview initialisation with no alignment. loadAlignment() method can
1497 // still be called to open new alignments.
1504 private void initLiveConnect()
1506 // try really hard to get the liveConnect thing working
1507 boolean notFailed = false;
1509 while (!notFailed && tries < 10)
1513 System.err.println("LiveConnect request thread going to sleep.");
1517 Thread.sleep(700 * (1 + tries));
1518 } catch (InterruptedException q)
1524 System.err.println("LiveConnect request thread woken up.");
1528 JSObject scriptObject = JSObject.getWindow(this);
1529 if (scriptObject.eval("navigator") != null)
1533 } catch (JSException jsex)
1535 System.err.println("Attempt " + tries
1536 + " to access LiveConnect javascript failed.");
1541 private void callInitCallback()
1543 String initjscallback = getParameter("oninit");
1544 if (initjscallback == null)
1548 initjscallback = initjscallback.trim();
1549 if (initjscallback.length() > 0)
1551 JSObject scriptObject = null;
1554 scriptObject = JSObject.getWindow(this);
1555 } catch (Exception ex)
1559 // try really hard to let the browser plugin know we want liveconnect
1562 if (scriptObject != null)
1566 // do onInit with the JS executor thread
1567 new JSFunctionExec(this).executeJavascriptFunction(true,
1568 initjscallback, null, "Calling oninit callback '"
1569 + initjscallback + "'.");
1570 } catch (Exception e)
1572 System.err.println("Exception when executing _oninit callback '"
1573 + initjscallback + "'.");
1574 e.printStackTrace();
1579 System.err.println("Not executing _oninit callback '"
1580 + initjscallback + "' - no scripting allowed.");
1586 * Initialises and displays a new java.awt.Frame
1589 * java.awt.Frame to be displayed
1591 * title of new frame
1593 * width if new frame
1595 * height of new frame
1597 public static void addFrame(final Frame frame, String title, int width,
1600 frame.setLocation(lastFrameX, lastFrameY);
1603 frame.setSize(width, height);
1604 frame.setTitle(title);
1605 frame.addWindowListener(new WindowAdapter()
1607 public void windowClosing(WindowEvent e)
1609 if (frame instanceof AlignFrame)
1611 AlignViewport vp = ((AlignFrame) frame).viewport;
1612 ((AlignFrame) frame).closeMenuItem_actionPerformed();
1613 if (vp.applet.currentAlignFrame == frame)
1615 vp.applet.currentAlignFrame = null;
1623 if (frame instanceof EmbmenuFrame)
1625 ((EmbmenuFrame) frame).destroyMenus();
1627 frame.setMenuBar(null);
1631 public void windowActivated(WindowEvent e)
1633 if (frame instanceof AlignFrame)
1635 ((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame;
1638 System.err.println("Activated window " + frame);
1642 super.windowActivated(e);
1645 * Probably not necessary to do this - see TODO above. (non-Javadoc)
1648 * java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent
1651 * public void windowDeactivated(WindowEvent e) { if (currentAlignFrame ==
1652 * frame) { currentAlignFrame = null; if (debug) {
1653 * System.err.println("Deactivated window "+frame); } }
1654 * super.windowDeactivated(e); }
1657 frame.setVisible(true);
1661 * This paints the background surrounding the "Launch Jalview button" <br>
1663 * If file given in parameter not found, displays error message
1668 public void paint(Graphics g)
1672 g.setColor(new Color(200, 200, 200));
1673 g.setColor(Color.cyan);
1674 g.fillRect(0, 0, getSize().width, getSize().height);
1675 g.setColor(Color.red);
1677 MessageManager.getString("label.jalview_cannot_open_file"),
1679 g.drawString("\"" + file + "\"", 5, 30);
1683 g.setColor(Color.black);
1684 g.setFont(new Font("Arial", Font.BOLD, 24));
1685 g.drawString(MessageManager.getString("label.jalview_applet"), 50,
1686 getSize().height / 2 - 30);
1687 g.drawString(MessageManager.getString("label.loading_data") + "...",
1688 50, getSize().height / 2);
1693 * get all components associated with the applet of the given type
1698 public Vector getAppletWindow(Class class1)
1700 Vector wnds = new Vector();
1701 Component[] cmp = getComponents();
1704 for (int i = 0; i < cmp.length; i++)
1706 if (class1.isAssignableFrom(cmp[i].getClass()))
1708 wnds.addElement(cmp);
1715 class LoadJmolThread extends Thread
1717 private boolean running = false;
1721 if (running || checkedForJmol)
1730 if (!System.getProperty("java.version").startsWith("1.1"))
1732 Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
1733 jmolAvailable = true;
1738 .println("Jmol not available - Using MCview for structures");
1740 } catch (java.lang.ClassNotFoundException ex)
1746 jmolAvailable = false;
1750 .println("Skipping Jmol check. Will use MCView (probably)");
1753 checkedForJmol = true;
1757 public boolean notFinished()
1759 return running || !checkedForJmol;
1763 class LoadingThread extends Thread
1766 * State variable: protocol for access to file source
1770 String _file; // alignment file or URL spec
1772 String _file2; // second alignment file or URL spec
1776 private void dbgMsg(String msg)
1778 if (JalviewLite.debug)
1780 System.err.println(msg);
1785 * update the protocol state variable for accessing the datasource located
1789 * @return possibly updated datasource string
1791 public String setProtocolState(String file)
1793 if (file.startsWith("PASTE"))
1795 file = file.substring(5);
1796 protocol = AppletFormatAdapter.PASTE;
1798 else if (inArchive(file))
1800 protocol = AppletFormatAdapter.CLASSLOADER;
1804 file = addProtocol(file);
1805 protocol = AppletFormatAdapter.URL;
1807 dbgMsg("Protocol identified as '" + protocol + "'");
1811 // public LoadingThread(String _file, JalviewLite _applet)
1813 // this._file = _file;
1814 // applet = _applet;
1817 public LoadingThread(String file, String file2, JalviewLite _applet)
1820 this._file2 = file2;
1826 LoadJmolThread jmolchecker = new LoadJmolThread();
1827 jmolchecker.start();
1828 while (jmolchecker.notFinished())
1830 // wait around until the Jmol check is complete.
1834 } catch (Exception e)
1839 // applet.callInitCallback();
1843 * Load the alignment and any related files as specified by applet
1846 private void startLoading()
1848 dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");
1850 dbgMsg("Loading started.");
1852 AlignFrame newAlignFrame = readAlignment(_file);
1853 AlignFrame newAlignFrame2 = readAlignment(_file2);
1854 if (newAlignFrame != null)
1856 addToDisplay(newAlignFrame, newAlignFrame2);
1857 loadTree(newAlignFrame);
1859 loadScoreFile(newAlignFrame);
1861 loadFeatures(newAlignFrame);
1863 loadAnnotations(newAlignFrame);
1865 loadJnetFile(newAlignFrame);
1867 loadPdbFiles(newAlignFrame);
1872 applet.remove(launcher);
1879 * Add an AlignFrame to the display; or if two are provided, a SplitFrame.
1884 public void addToDisplay(AlignFrame af, AlignFrame af2)
1888 af.addToDisplay(embedded);
1892 SplitFrame sf = new SplitFrame(af, af2);
1893 sf.addToDisplay(embedded, JalviewLite.this);
1898 * Read the alignment file (from URL, text 'paste', or archive by
1903 protected AlignFrame readAlignment(String fileParam)
1905 if (fileParam == null)
1909 String resolvedFile = setProtocolState(fileParam);
1910 String format = new IdentifyFile().Identify(resolvedFile, protocol);
1911 dbgMsg("File identified as '" + format + "'");
1912 AlignmentI al = null;
1915 al = new AppletFormatAdapter().readFile(resolvedFile, protocol, format);
1916 if ((al != null) && (al.getHeight() > 0))
1918 dbgMsg("Successfully loaded file.");
1919 al.setDataset(null);
1920 AlignFrame newAlignFrame = new AlignFrame(al, applet,
1921 resolvedFile, embedded, false);
1922 newAlignFrame.setTitle(resolvedFile);
1923 if (initialAlignFrame == null)
1925 initialAlignFrame = newAlignFrame;
1927 // update the focus.
1928 currentAlignFrame = newAlignFrame;
1930 if (protocol == AppletFormatAdapter.PASTE)
1932 newAlignFrame.setTitle(MessageManager.formatMessage(
1933 "label.sequences_from", new Object[]
1934 { applet.getDocumentBase().toString() }));
1937 newAlignFrame.statusBar.setText(MessageManager.formatMessage(
1938 "label.successfully_loaded_file", new Object[]
1941 return newAlignFrame;
1943 } catch (java.io.IOException ex)
1945 dbgMsg("File load exception.");
1946 ex.printStackTrace();
1951 FileParse fp = new FileParse(resolvedFile, protocol);
1953 dbgMsg(">>>Dumping contents of '" + resolvedFile + "' " + "("
1955 while ((ln = fp.nextLine()) != null)
1959 dbgMsg(">>>Dump finished.");
1960 } catch (Exception e)
1963 .println("Exception when trying to dump the content of the file parameter.");
1964 e.printStackTrace();
1972 * Load PDBFiles if any specified by parameter(s). Returns true if loaded,
1978 protected boolean loadPdbFiles(AlignFrame alignFrame)
1980 boolean result = false;
1982 * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6 -
1983 * related to JAL-434
1986 applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",
1989 * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
1992 * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
1994 * <param name="PDBfile3" value="1q0o Q45135_9MICO">
1997 int pdbFileCount = 0;
1998 // Accumulate pdbs here if they are heading for the same view (if
1999 // alignPdbStructures is true)
2000 Vector pdbs = new Vector();
2001 // create a lazy matcher if we're asked to
2002 jalview.analysis.SequenceIdMatcher matcher = (applet
2003 .getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher(
2004 alignFrame.getAlignViewport().getAlignment()
2005 .getSequencesArray()) : null;
2010 if (pdbFileCount > 0)
2012 param = applet.getParameter("PDBFILE" + pdbFileCount);
2016 param = applet.getParameter("PDBFILE");
2021 PDBEntry pdb = new PDBEntry();
2024 SequenceI[] seqs = null;
2025 String[] chains = null;
2027 StringTokenizer st = new StringTokenizer(param, " ");
2029 if (st.countTokens() < 2)
2031 String sequence = applet.getParameter("PDBSEQ");
2032 if (sequence != null)
2034 seqs = new SequenceI[]
2035 { matcher == null ? (Sequence) alignFrame.getAlignViewport()
2036 .getAlignment().findName(sequence) : matcher
2037 .findIdMatch(sequence) };
2043 param = st.nextToken();
2044 Vector tmp = new Vector();
2045 Vector tmp2 = new Vector();
2047 while (st.hasMoreTokens())
2049 seqstring = st.nextToken();
2050 StringTokenizer st2 = new StringTokenizer(seqstring, "=");
2051 if (st2.countTokens() > 1)
2053 // This is the chain
2054 tmp2.addElement(st2.nextToken());
2055 seqstring = st2.nextToken();
2057 tmp.addElement(matcher == null ? (Sequence) alignFrame
2058 .getAlignViewport().getAlignment()
2059 .findName(seqstring) : matcher.findIdMatch(seqstring));
2062 seqs = new SequenceI[tmp.size()];
2064 if (tmp2.size() == tmp.size())
2066 chains = new String[tmp2.size()];
2067 tmp2.copyInto(chains);
2070 param = setProtocolState(param);
2072 if (// !jmolAvailable
2074 protocol == AppletFormatAdapter.CLASSLOADER && !useXtrnalSviewer)
2076 // Re: JAL-357 : the bug isn't a problem if we are using an
2078 // TODO: verify this Re:
2079 // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
2080 // This exception preserves the current behaviour where, even if
2081 // the local pdb file was identified in the class loader
2082 protocol = AppletFormatAdapter.URL; // this is probably NOT
2084 param = addProtocol(param); //
2091 for (int i = 0; i < seqs.length; i++)
2093 if (seqs[i] != null)
2095 ((Sequence) seqs[i]).addPDBId(pdb);
2096 StructureSelectionManager.getStructureSelectionManager(
2097 applet).registerPDBEntry(pdb);
2101 if (JalviewLite.debug)
2103 // this may not really be a problem but we give a warning
2106 .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
2112 if (!alignPdbStructures)
2114 alignFrame.newStructureView(applet, pdb, seqs, chains,
2119 pdbs.addElement(new Object[]
2120 { pdb, seqs, chains, new String(protocol) });
2126 } while (param != null || pdbFileCount < 10);
2127 if (pdbs.size() > 0)
2129 SequenceI[][] seqs = new SequenceI[pdbs.size()][];
2130 PDBEntry[] pdb = new PDBEntry[pdbs.size()];
2131 String[][] chains = new String[pdbs.size()][];
2132 String[] protocols = new String[pdbs.size()];
2133 for (int pdbsi = 0, pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)
2135 Object[] o = (Object[]) pdbs.elementAt(pdbsi);
2136 pdb[pdbsi] = (PDBEntry) o[0];
2137 seqs[pdbsi] = (SequenceI[]) o[1];
2138 chains[pdbsi] = (String[]) o[2];
2139 protocols[pdbsi] = (String) o[3];
2141 alignFrame.alignedStructureView(applet, pdb, seqs, chains,
2149 * Load in a Jnetfile if specified by parameter. Returns true if loaded,
2155 protected boolean loadJnetFile(AlignFrame alignFrame)
2157 boolean result = false;
2158 String param = applet.getParameter("jnetfile");
2163 param = setProtocolState(param);
2164 JPredFile predictions = new JPredFile(param, protocol);
2165 JnetAnnotationMaker.add_annotation(predictions,
2166 alignFrame.viewport.getAlignment(), 0, false);
2167 // false == do not add sequence profile from concise output
2168 SequenceI repseq = alignFrame.viewport.getAlignment()
2170 alignFrame.viewport.getAlignment().setSeqrep(repseq);
2171 ColumnSelection cs = new ColumnSelection();
2172 cs.hideInsertionsFor(repseq);
2173 alignFrame.viewport.setColumnSelection(cs);
2174 alignFrame.alignPanel.fontChanged();
2175 alignFrame.alignPanel.setScrollValues(0, 0);
2177 } catch (Exception ex)
2179 ex.printStackTrace();
2186 * Load annotations if specified by parameter. Returns true if loaded, else
2192 protected boolean loadAnnotations(AlignFrame alignFrame)
2194 boolean result = false;
2195 String param = applet.getParameter("annotations");
2198 param = setProtocolState(param);
2200 if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
2203 alignFrame.alignPanel.fontChanged();
2204 alignFrame.alignPanel.setScrollValues(0, 0);
2210 .println("Annotations were not added from annotation file '"
2218 * Load features file and view settings as specified by parameters. Returns
2219 * true if features were loaded, else false.
2224 protected boolean loadFeatures(AlignFrame alignFrame)
2226 boolean result = false;
2227 // ///////////////////////////
2228 // modify display of features
2229 // we do this before any features have been loaded, ensuring any hidden
2230 // groups are hidden when features first displayed
2232 // hide specific groups
2234 String param = applet.getParameter("hidefeaturegroups");
2237 alignFrame.setFeatureGroupState(separatorListToArray(param), false);
2238 // applet.setFeatureGroupStateOn(newAlignFrame, param, false);
2240 // show specific groups
2241 param = applet.getParameter("showfeaturegroups");
2244 alignFrame.setFeatureGroupState(separatorListToArray(param), true);
2245 // applet.setFeatureGroupStateOn(newAlignFrame, param, true);
2247 // and now load features
2248 param = applet.getParameter("features");
2251 param = setProtocolState(param);
2253 result = alignFrame.parseFeaturesFile(param, protocol);
2256 param = applet.getParameter("showFeatureSettings");
2257 if (param != null && param.equalsIgnoreCase(TRUE))
2259 alignFrame.viewport.setShowSequenceFeatures(true);
2260 new FeatureSettings(alignFrame.alignPanel);
2266 * Load a score file if specified by parameter. Returns true if file was
2267 * loaded, else false.
2271 protected boolean loadScoreFile(AlignFrame alignFrame)
2273 boolean result = false;
2274 String sScoreFile = applet.getParameter("scoreFile");
2275 if (sScoreFile != null && !"".equals(sScoreFile))
2282 .println("Attempting to load T-COFFEE score file from the scoreFile parameter");
2284 result = alignFrame.loadScoreFile(sScoreFile);
2288 .println("Failed to parse T-COFFEE parameter as a valid score file ('"
2289 + sScoreFile + "')");
2291 } catch (Exception e)
2293 System.err.printf("Cannot read score file: '%s'. Cause: %s \n",
2294 sScoreFile, e.getMessage());
2301 * Load a tree for the alignment if specified by parameter. Returns true if
2302 * a tree was loaded, else false.
2307 protected boolean loadTree(AlignFrame alignFrame)
2309 boolean result = false;
2310 String treeFile = applet.getParameter("tree");
2311 if (treeFile == null)
2313 treeFile = applet.getParameter("treeFile");
2316 if (treeFile != null)
2320 treeFile = setProtocolState(treeFile);
2321 NewickFile fin = new NewickFile(treeFile, protocol);
2324 if (fin.getTree() != null)
2326 alignFrame.loadTree(fin, treeFile);
2328 dbgMsg("Successfully imported tree.");
2332 dbgMsg("Tree parameter did not resolve to a valid tree.");
2334 } catch (Exception ex)
2336 ex.printStackTrace();
2343 * Discovers whether the given file is in the Applet Archive
2349 boolean inArchive(String file)
2351 // This might throw a security exception in certain browsers
2352 // Netscape Communicator for instance.
2355 boolean rtn = (getClass().getResourceAsStream("/" + file) != null);
2358 System.err.println("Resource '" + file + "' was "
2359 + (rtn ? "" : "not") + " located by classloader.");
2362 } catch (Exception ex)
2364 System.out.println("Exception checking resources: " + file + " "
2371 * If the file is not already in URL format, tries to locate it by resolving
2377 String addProtocol(final String file)
2379 if (file.indexOf("://") == -1)
2382 * Try relative to document base
2384 String url = applet.resolveUrlForLocalOrAbsolute(file,
2390 System.err.println("Prepended document base for resource: '"
2397 * Try relative to codebase
2399 url = applet.resolveUrlForLocalOrAbsolute(file, getCodeBase());
2404 System.err.println("Prepended codebase for resource: '" + file
2412 * Not resolved, leave unchanged
2418 * Returns true if an input stream can be opened on the specified URL, else
2424 private boolean urlExists(String url)
2426 InputStream is = null;
2429 is = new URL(url).openStream();
2434 } catch (Exception x)
2444 } catch (IOException e)
2455 * @return the default alignFrame acted on by the public applet methods. May
2456 * return null with an error message on System.err indicating the
2459 public AlignFrame getDefaultTargetFrame()
2461 if (currentAlignFrame != null)
2463 return currentAlignFrame;
2465 if (initialAlignFrame != null)
2467 return initialAlignFrame;
2470 .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
2475 * separator used for separatorList
2477 protected String separator = "" + ((char) 0x00AC); // the default used to be
2478 // '|' but many sequence
2479 // IDS include pipes.
2482 * set to enable the URL based javascript execution mechanism
2484 public boolean jsfallbackEnabled = false;
2487 * parse the string into a list
2490 * @return elements separated by separator
2492 public String[] separatorListToArray(String list)
2494 return separatorListToArray(list, separator);
2498 * parse the string into a list
2502 * @return elements separated by separator
2504 public String[] separatorListToArray(String list, String separator)
2506 // note separator local variable intentionally masks object field
2507 int seplen = separator.length();
2508 if (list == null || list.equals("") || list.equals(separator))
2512 java.util.Vector jv = new Vector();
2514 while ((pos = list.indexOf(separator, cp)) > cp)
2516 jv.addElement(list.substring(cp, pos));
2519 if (cp < list.length())
2521 String c = list.substring(cp);
2522 if (!c.equals(separator))
2529 String[] v = new String[jv.size()];
2530 for (int i = 0; i < v.length; i++)
2532 v[i] = (String) jv.elementAt(i);
2534 jv.removeAllElements();
2537 System.err.println("Array from '" + separator
2538 + "' separated List:\n" + v.length);
2539 for (int i = 0; i < v.length; i++)
2541 System.err.println("item " + i + " '" + v[i] + "'");
2548 System.err.println("Empty Array from '" + separator
2549 + "' separated List");
2555 * concatenate the list with separator
2558 * @return concatenated string
2560 public String arrayToSeparatorList(String[] list)
2562 return arrayToSeparatorList(list, separator);
2566 * concatenate the list with separator
2570 * @return concatenated string
2572 public String arrayToSeparatorList(String[] list, String separator)
2574 StringBuffer v = new StringBuffer();
2575 if (list != null && list.length > 0)
2577 for (int i = 0, iSize = list.length; i < iSize; i++)
2579 if (list[i] != null)
2583 v.append(separator);
2590 System.err.println("Returning '" + separator
2591 + "' separated List:\n");
2592 System.err.println(v);
2594 return v.toString();
2598 System.err.println("Returning empty '" + separator
2599 + "' separated List\n");
2601 return "" + separator;
2607 * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
2609 public String getFeatureGroups()
2611 String lst = arrayToSeparatorList(getDefaultTargetFrame()
2612 .getFeatureGroups());
2620 * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame
2623 public String getFeatureGroupsOn(AlignFrame alf)
2625 String lst = arrayToSeparatorList(alf.getFeatureGroups());
2632 * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)
2634 public String getFeatureGroupsOfState(boolean visible)
2636 return arrayToSeparatorList(getDefaultTargetFrame()
2637 .getFeatureGroupsOfState(visible));
2644 * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui
2645 * .AlignFrame, boolean)
2647 public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
2649 return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
2655 * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui.
2656 * AlignFrame, java.lang.String, boolean)
2658 public void setFeatureGroupStateOn(final AlignFrame alf,
2659 final String groups, boolean state)
2661 final boolean st = state;// !(state==null || state.equals("") ||
2662 // state.toLowerCase().equals("false"));
2663 java.awt.EventQueue.invokeLater(new Runnable()
2668 alf.setFeatureGroupState(separatorListToArray(groups), st);
2676 * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupState(java.lang.String,
2679 public void setFeatureGroupState(String groups, boolean state)
2681 setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
2687 * @see jalview.bin.JalviewLiteJsApi#getSeparator()
2689 public String getSeparator()
2697 * @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String)
2699 public void setSeparator(String separator)
2701 if (separator == null || separator.length() < 1)
2704 separator = "" + ((char) 0x00AC);
2706 this.separator = separator;
2709 System.err.println("Default Separator now: '" + separator + "'");
2714 * get boolean value of applet parameter 'name' and return default if
2715 * parameter is not set
2720 * the value to return otherwise
2721 * @return true or false
2723 public boolean getDefaultParameter(String name, boolean def)
2726 if ((stn = getParameter(name)) == null)
2730 if (stn.toLowerCase().equals(TRUE))
2740 * @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame,
2741 * java.lang.String, java.lang.String, java.lang.String)
2743 public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
2744 String pdbEntryString, String pdbFile)
2746 return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);
2749 protected void setAlignPdbStructures(boolean alignPdbStructures)
2751 this.alignPdbStructures = alignPdbStructures;
2754 public boolean isAlignPdbStructures()
2756 return alignPdbStructures;
2761 // callInitCallback();
2764 private Hashtable<String, long[]> jshashes = new Hashtable<String, long[]>();
2766 private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<String, Hashtable<String, String[]>>();
2768 public void setJsMessageSet(String messageclass, String viewId,
2769 String[] colcommands)
2771 Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
2774 msgset = new Hashtable<String, String[]>();
2775 jsmessages.put(messageclass, msgset);
2777 msgset.put(viewId, colcommands);
2778 long[] l = new long[colcommands.length];
2779 for (int i = 0; i < colcommands.length; i++)
2781 l[i] = colcommands[i].hashCode();
2783 jshashes.put(messageclass + "|" + viewId, l);
2789 * @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String,
2792 public String getJsMessage(String messageclass, String viewId)
2794 Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
2797 String[] msgs = msgset.get(viewId);
2800 for (int i = 0; i < msgs.length; i++)
2802 if (msgs[i] != null)
2814 public boolean isJsMessageSetChanged(String string, String string2,
2815 String[] colcommands)
2817 long[] l = jshashes.get(string + "|" + string2);
2818 if (l == null && colcommands != null)
2822 for (int i = 0; i < colcommands.length; i++)
2824 if (l[i] != colcommands[i].hashCode())
2832 private Vector jsExecQueue = new Vector();
2834 public Vector getJsExecQueue()
2839 public void setExecutor(JSFunctionExec jsFunctionExec2)
2841 jsFunctionExec = jsFunctionExec2;
2845 * return the given colour value parameter or the given default if parameter
2852 public Color getDefaultColourParameter(String colparam, Color defcolour)
2854 String colprop = getParameter(colparam);
2855 if (colprop == null || colprop.trim().length() == 0)
2859 Color col = jalview.schemes.ColourSchemeProperty
2860 .getAWTColorFromName(colprop);
2865 col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
2866 } catch (Exception ex)
2868 System.err.println("Couldn't parse '" + colprop
2869 + "' as a colour for " + colparam);
2873 return (col == null) ? defcolour : col;
2877 public void openJalviewHelpUrl()
2879 String helpUrl = getParameter("jalviewhelpurl");
2880 if (helpUrl == null || helpUrl.trim().length() < 5)
2882 helpUrl = "http://www.jalview.org/help.html";
2884 showURL(helpUrl, "HELP");
2888 * form a complete URL given a path to a resource and a reference location on
2892 * - an absolute path on the same server as localref or a document
2893 * located relative to localref
2895 * - a URL on the same server as url
2896 * @return a complete URL for the resource located by url
2898 private String resolveUrlForLocalOrAbsolute(String url, URL localref)
2900 String codebase = localref.toString();
2901 if (url.indexOf("/") == 0)
2903 url = codebase.substring(0, codebase.length()
2904 - localref.getFile().length())
2909 url = localref + url;
2915 * open a URL in the browser - resolving it according to relative refs and
2916 * coping with javascript: protocol if necessary.
2921 public void showURL(String url, String target)
2925 if (url.indexOf(":") == -1)
2927 // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
2929 // Should really use docbase, not codebase.
2931 url = resolveUrlForLocalOrAbsolute(
2933 prepend = getDefaultParameter("resolvetocodebase", false) ? getDocumentBase()
2938 .println("Show url (prepended "
2940 + " - toggle resolvetocodebase if code/docbase resolution is wrong): "
2948 System.err.println("Show url: " + url);
2951 if (url.indexOf("javascript:") == 0)
2953 // no target for the javascript context
2954 getAppletContext().showDocument(new java.net.URL(url));
2958 getAppletContext().showDocument(new java.net.URL(url), target);
2960 } catch (Exception ex)
2962 ex.printStackTrace();
2967 * bind structures in a viewer to any matching sequences in an alignFrame (use
2968 * sequenceIds to limit scope of search to specific sequences)
2972 * @param sequenceIds
2973 * @return TODO: consider making an exception structure for indicating when
2974 * binding fails public SequenceStructureBinding
2975 * addStructureViewInstance( AlignFrame alFrame, Object viewer, String
2978 * if (sequenceIds != null && sequenceIds.length() > 0) { return
2979 * alFrame.addStructureViewInstance(viewer,
2980 * separatorListToArray(sequenceIds)); } else { return
2981 * alFrame.addStructureViewInstance(viewer, null); } // return null; }