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.FileParse;
41 import jalview.io.IdentifyFile;
42 import jalview.io.JPredFile;
43 import jalview.io.JnetAnnotationMaker;
44 import jalview.io.NewickFile;
45 import jalview.javascript.JSFunctionExec;
46 import jalview.javascript.JalviewLiteJsApi;
47 import jalview.javascript.JsCallBack;
48 import jalview.structure.SelectionListener;
49 import jalview.structure.StructureSelectionManager;
50 import jalview.util.MessageManager;
52 import java.applet.Applet;
53 import java.awt.Button;
54 import java.awt.Color;
55 import java.awt.Component;
56 import java.awt.EventQueue;
58 import java.awt.Frame;
59 import java.awt.Graphics;
60 import java.awt.event.ActionEvent;
61 import java.awt.event.WindowAdapter;
62 import java.awt.event.WindowEvent;
63 import java.io.BufferedReader;
64 import java.io.IOException;
65 import java.io.InputStream;
66 import java.io.InputStreamReader;
68 import java.util.Hashtable;
69 import java.util.List;
70 import java.util.StringTokenizer;
71 import java.util.Vector;
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)
850 AlignmentI al = null;
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 = null;
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 = "applet";
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().equals(TRUE);
1391 * if true disable the check for jmol
1393 String chkforJmol = getParameter("nojmol");
1394 if (chkforJmol != null)
1396 checkForJmol = !chkforJmol.equals(TRUE);
1399 * get the separator parameter if present
1401 String sep = getParameter("separator");
1404 if (sep.length() > 0)
1409 System.err.println("Separator set to '" + separator + "'");
1416 .getString("error.invalid_separator_parameter"));
1422 String param = getParameter("RGB");
1428 r = Integer.parseInt(param.substring(0, 2), 16);
1429 g = Integer.parseInt(param.substring(2, 4), 16);
1430 b = Integer.parseInt(param.substring(4, 6), 16);
1431 } catch (Exception ex)
1438 param = getParameter("label");
1441 launcher.setLabel(param);
1444 setBackground(new Color(r, g, b));
1446 file = getParameter("file");
1450 // Maybe the sequences are added as parameters
1451 StringBuffer data = new StringBuffer("PASTE");
1453 while ((file = getParameter("sequence" + i)) != null)
1455 data.append(file.toString() + "\n");
1458 if (data.length() > 5)
1460 file = data.toString();
1463 if (getDefaultParameter("enableSplitFrame", true))
1465 file2 = getParameter("file2");
1468 embedded = TRUE.equalsIgnoreCase(getParameter("embedded"));
1471 LoadingThread loader = new LoadingThread(file, file2, this);
1474 else if (file != null)
1477 * Start the applet immediately or show a button to start it
1479 if (FALSE.equalsIgnoreCase(getParameter("showbutton")))
1481 LoadingThread loader = new LoadingThread(file, file2, this);
1487 launcher.addActionListener(new java.awt.event.ActionListener()
1489 public void actionPerformed(ActionEvent e)
1491 LoadingThread loader = new LoadingThread(file, file2,
1500 // jalview initialisation with no alignment. loadAlignment() method can
1501 // still be called to open new alignments.
1508 private void initLiveConnect()
1510 // try really hard to get the liveConnect thing working
1511 boolean notFailed = false;
1513 while (!notFailed && tries < 10)
1517 System.err.println("LiveConnect request thread going to sleep.");
1521 Thread.sleep(700 * (1 + tries));
1522 } catch (InterruptedException q)
1528 System.err.println("LiveConnect request thread woken up.");
1532 JSObject scriptObject = JSObject.getWindow(this);
1533 if (scriptObject.eval("navigator") != null)
1537 } catch (Exception jsex)
1539 System.err.println("Attempt " + tries
1540 + " to access LiveConnect javascript failed.");
1545 private void callInitCallback()
1547 String initjscallback = getParameter("oninit");
1548 if (initjscallback == null)
1552 initjscallback = initjscallback.trim();
1553 if (initjscallback.length() > 0)
1555 JSObject scriptObject = null;
1558 scriptObject = JSObject.getWindow(this);
1559 } catch (Exception ex)
1563 // try really hard to let the browser plugin know we want liveconnect
1566 if (scriptObject != null)
1570 // do onInit with the JS executor thread
1571 new JSFunctionExec(this).executeJavascriptFunction(true,
1572 initjscallback, null, "Calling oninit callback '"
1573 + initjscallback + "'.");
1574 } catch (Exception e)
1576 System.err.println("Exception when executing _oninit callback '"
1577 + initjscallback + "'.");
1578 e.printStackTrace();
1583 System.err.println("Not executing _oninit callback '"
1584 + initjscallback + "' - no scripting allowed.");
1590 * Initialises and displays a new java.awt.Frame
1593 * java.awt.Frame to be displayed
1595 * title of new frame
1597 * width if new frame
1599 * height of new frame
1601 public static void addFrame(final Frame frame, String title, int width,
1604 frame.setLocation(lastFrameX, lastFrameY);
1607 frame.setSize(width, height);
1608 frame.setTitle(title);
1609 frame.addWindowListener(new WindowAdapter()
1611 public void windowClosing(WindowEvent e)
1613 if (frame instanceof AlignFrame)
1615 AlignViewport vp = ((AlignFrame) frame).viewport;
1616 ((AlignFrame) frame).closeMenuItem_actionPerformed();
1617 if (vp.applet.currentAlignFrame == frame)
1619 vp.applet.currentAlignFrame = null;
1627 if (frame instanceof EmbmenuFrame)
1629 ((EmbmenuFrame) frame).destroyMenus();
1631 frame.setMenuBar(null);
1635 public void windowActivated(WindowEvent e)
1637 if (frame instanceof AlignFrame)
1639 ((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame;
1642 System.err.println("Activated window " + frame);
1646 super.windowActivated(e);
1649 * Probably not necessary to do this - see TODO above. (non-Javadoc)
1652 * java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent
1655 * public void windowDeactivated(WindowEvent e) { if (currentAlignFrame ==
1656 * frame) { currentAlignFrame = null; if (debug) {
1657 * System.err.println("Deactivated window "+frame); } }
1658 * super.windowDeactivated(e); }
1661 frame.setVisible(true);
1665 * This paints the background surrounding the "Launch Jalview button" <br>
1667 * If file given in parameter not found, displays error message
1672 public void paint(Graphics g)
1676 g.setColor(new Color(200, 200, 200));
1677 g.setColor(Color.cyan);
1678 g.fillRect(0, 0, getSize().width, getSize().height);
1679 g.setColor(Color.red);
1681 MessageManager.getString("label.jalview_cannot_open_file"),
1683 g.drawString("\"" + file + "\"", 5, 30);
1687 g.setColor(Color.black);
1688 g.setFont(new Font("Arial", Font.BOLD, 24));
1689 g.drawString(MessageManager.getString("label.jalview_applet"), 50,
1690 getSize().height / 2 - 30);
1691 g.drawString(MessageManager.getString("label.loading_data") + "...",
1692 50, getSize().height / 2);
1697 * get all components associated with the applet of the given type
1702 public Vector getAppletWindow(Class class1)
1704 Vector wnds = new Vector();
1705 Component[] cmp = getComponents();
1708 for (int i = 0; i < cmp.length; i++)
1710 if (class1.isAssignableFrom(cmp[i].getClass()))
1712 wnds.addElement(cmp);
1719 class LoadJmolThread extends Thread
1721 private boolean running = false;
1725 if (running || checkedForJmol)
1734 if (!System.getProperty("java.version").startsWith("1.1"))
1736 Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
1737 jmolAvailable = true;
1742 .println("Jmol not available - Using MCview for structures");
1744 } catch (java.lang.ClassNotFoundException ex)
1750 jmolAvailable = false;
1754 .println("Skipping Jmol check. Will use MCView (probably)");
1757 checkedForJmol = true;
1761 public boolean notFinished()
1763 return running || !checkedForJmol;
1767 class LoadingThread extends Thread
1770 * State variable: protocol for access to file source
1774 String _file; // alignment file or URL spec
1776 String _file2; // second alignment file or URL spec
1780 private void dbgMsg(String msg)
1782 if (JalviewLite.debug)
1784 System.err.println(msg);
1789 * update the protocol state variable for accessing the datasource located
1793 * @return possibly updated datasource string
1795 public String setProtocolState(String file)
1797 if (file.startsWith("PASTE"))
1799 file = file.substring(5);
1800 protocol = AppletFormatAdapter.PASTE;
1802 else if (inArchive(file))
1804 protocol = AppletFormatAdapter.CLASSLOADER;
1808 file = addProtocol(file);
1809 protocol = AppletFormatAdapter.URL;
1811 dbgMsg("Protocol identified as '" + protocol + "'");
1815 public LoadingThread(String file, String file2, JalviewLite _applet)
1818 this._file2 = file2;
1824 LoadJmolThread jmolchecker = new LoadJmolThread();
1825 jmolchecker.start();
1826 while (jmolchecker.notFinished())
1828 // wait around until the Jmol check is complete.
1832 } catch (Exception e)
1837 // applet.callInitCallback();
1841 * Load the alignment and any related files as specified by applet
1844 private void startLoading()
1846 dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");
1848 dbgMsg("Loading started.");
1850 AlignFrame newAlignFrame = readAlignment(_file);
1851 AlignFrame newAlignFrame2 = readAlignment(_file2);
1852 if (newAlignFrame != null)
1854 addToDisplay(newAlignFrame, newAlignFrame2);
1855 loadTree(newAlignFrame);
1857 loadScoreFile(newAlignFrame);
1859 loadFeatures(newAlignFrame);
1861 loadAnnotations(newAlignFrame);
1863 loadJnetFile(newAlignFrame);
1865 loadPdbFiles(newAlignFrame);
1870 applet.remove(launcher);
1877 * Add an AlignFrame to the display; or if two are provided, a SplitFrame.
1882 public void addToDisplay(AlignFrame af, AlignFrame af2)
1886 AlignmentI al1 = af.viewport.getAlignment();
1887 AlignmentI al2 = af2.viewport.getAlignment();
1888 if (AlignmentUtils.isMappable(al1, al2))
1890 SplitFrame sf = new SplitFrame(af, af2);
1891 sf.addToDisplay(embedded, JalviewLite.this);
1896 String msg = "Could not map any sequence in " + af2.getTitle()
1898 + (al1.isNucleotide() ? "protein product" : "cDNA")
1899 + " for " + af.getTitle();
1900 System.err.println(msg);
1904 af.addToDisplay(embedded);
1908 * Read the alignment file (from URL, text 'paste', or archive by
1913 protected AlignFrame readAlignment(String fileParam)
1915 if (fileParam == null)
1919 String resolvedFile = setProtocolState(fileParam);
1920 String format = new IdentifyFile().Identify(resolvedFile, protocol);
1921 dbgMsg("File identified as '" + format + "'");
1922 AlignmentI al = null;
1925 al = new AppletFormatAdapter().readFile(resolvedFile, protocol,
1927 if ((al != null) && (al.getHeight() > 0))
1929 dbgMsg("Successfully loaded file.");
1930 al.setDataset(null);
1931 AlignFrame newAlignFrame = new AlignFrame(al, applet,
1932 resolvedFile, embedded, false);
1933 newAlignFrame.setTitle(resolvedFile);
1934 if (initialAlignFrame == null)
1936 initialAlignFrame = newAlignFrame;
1938 // update the focus.
1939 currentAlignFrame = newAlignFrame;
1941 if (protocol == AppletFormatAdapter.PASTE)
1943 newAlignFrame.setTitle(MessageManager.formatMessage(
1944 "label.sequences_from", new Object[] { applet
1945 .getDocumentBase().toString() }));
1948 newAlignFrame.statusBar.setText(MessageManager.formatMessage(
1949 "label.successfully_loaded_file",
1950 new Object[] { resolvedFile }));
1952 return newAlignFrame;
1954 } catch (java.io.IOException ex)
1956 dbgMsg("File load exception.");
1957 ex.printStackTrace();
1962 FileParse fp = new FileParse(resolvedFile, protocol);
1964 dbgMsg(">>>Dumping contents of '" + resolvedFile + "' " + "("
1966 while ((ln = fp.nextLine()) != null)
1970 dbgMsg(">>>Dump finished.");
1971 } catch (Exception e)
1974 .println("Exception when trying to dump the content of the file parameter.");
1975 e.printStackTrace();
1983 * Load PDBFiles if any specified by parameter(s). Returns true if loaded,
1989 protected boolean loadPdbFiles(AlignFrame alignFrame)
1991 boolean result = false;
1993 * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6 -
1994 * related to JAL-434
1997 applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",
2000 * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
2003 * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
2005 * <param name="PDBfile3" value="1q0o Q45135_9MICO">
2008 int pdbFileCount = 0;
2009 // Accumulate pdbs here if they are heading for the same view (if
2010 // alignPdbStructures is true)
2011 Vector pdbs = new Vector();
2012 // create a lazy matcher if we're asked to
2013 jalview.analysis.SequenceIdMatcher matcher = (applet
2014 .getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher(
2015 alignFrame.getAlignViewport().getAlignment()
2016 .getSequencesArray()) : null;
2021 if (pdbFileCount > 0)
2023 param = applet.getParameter("PDBFILE" + pdbFileCount);
2027 param = applet.getParameter("PDBFILE");
2032 PDBEntry pdb = new PDBEntry();
2035 SequenceI[] seqs = null;
2036 String[] chains = null;
2038 StringTokenizer st = new StringTokenizer(param, " ");
2040 if (st.countTokens() < 2)
2042 String sequence = applet.getParameter("PDBSEQ");
2043 if (sequence != null)
2045 seqs = new SequenceI[] { matcher == null ? (Sequence) alignFrame
2046 .getAlignViewport().getAlignment().findName(sequence)
2047 : matcher.findIdMatch(sequence) };
2053 param = st.nextToken();
2054 Vector tmp = new Vector();
2055 Vector tmp2 = new Vector();
2057 while (st.hasMoreTokens())
2059 seqstring = st.nextToken();
2060 StringTokenizer st2 = new StringTokenizer(seqstring, "=");
2061 if (st2.countTokens() > 1)
2063 // This is the chain
2064 tmp2.addElement(st2.nextToken());
2065 seqstring = st2.nextToken();
2067 tmp.addElement(matcher == null ? (Sequence) alignFrame
2068 .getAlignViewport().getAlignment()
2069 .findName(seqstring) : matcher.findIdMatch(seqstring));
2072 seqs = new SequenceI[tmp.size()];
2074 if (tmp2.size() == tmp.size())
2076 chains = new String[tmp2.size()];
2077 tmp2.copyInto(chains);
2080 param = setProtocolState(param);
2082 if (// !jmolAvailable
2084 protocol == AppletFormatAdapter.CLASSLOADER && !useXtrnalSviewer)
2086 // Re: JAL-357 : the bug isn't a problem if we are using an
2088 // TODO: verify this Re:
2089 // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
2090 // This exception preserves the current behaviour where, even if
2091 // the local pdb file was identified in the class loader
2092 protocol = AppletFormatAdapter.URL; // this is probably NOT
2094 param = addProtocol(param); //
2101 for (int i = 0; i < seqs.length; i++)
2103 if (seqs[i] != null)
2105 ((Sequence) seqs[i]).addPDBId(pdb);
2106 StructureSelectionManager.getStructureSelectionManager(
2107 applet).registerPDBEntry(pdb);
2111 if (JalviewLite.debug)
2113 // this may not really be a problem but we give a warning
2116 .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
2122 if (!alignPdbStructures)
2124 alignFrame.newStructureView(applet, pdb, seqs, chains,
2129 pdbs.addElement(new Object[] { pdb, seqs, chains,
2130 new String(protocol) });
2136 } while (param != null || pdbFileCount < 10);
2137 if (pdbs.size() > 0)
2139 SequenceI[][] seqs = new SequenceI[pdbs.size()][];
2140 PDBEntry[] pdb = new PDBEntry[pdbs.size()];
2141 String[][] chains = new String[pdbs.size()][];
2142 String[] protocols = new String[pdbs.size()];
2143 for (int pdbsi = 0, pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)
2145 Object[] o = (Object[]) pdbs.elementAt(pdbsi);
2146 pdb[pdbsi] = (PDBEntry) o[0];
2147 seqs[pdbsi] = (SequenceI[]) o[1];
2148 chains[pdbsi] = (String[]) o[2];
2149 protocols[pdbsi] = (String) o[3];
2151 alignFrame.alignedStructureView(applet, pdb, seqs, chains,
2159 * Load in a Jnetfile if specified by parameter. Returns true if loaded,
2165 protected boolean loadJnetFile(AlignFrame alignFrame)
2167 boolean result = false;
2168 String param = applet.getParameter("jnetfile");
2173 param = setProtocolState(param);
2174 JPredFile predictions = new JPredFile(param, protocol);
2175 JnetAnnotationMaker.add_annotation(predictions,
2176 alignFrame.viewport.getAlignment(), 0, false);
2177 // false == do not add sequence profile from concise output
2178 SequenceI repseq = alignFrame.viewport.getAlignment()
2180 alignFrame.viewport.getAlignment().setSeqrep(repseq);
2181 ColumnSelection cs = new ColumnSelection();
2182 cs.hideInsertionsFor(repseq);
2183 alignFrame.viewport.setColumnSelection(cs);
2184 alignFrame.alignPanel.fontChanged();
2185 alignFrame.alignPanel.setScrollValues(0, 0);
2187 } catch (Exception ex)
2189 ex.printStackTrace();
2196 * Load annotations if specified by parameter. Returns true if loaded, else
2202 protected boolean loadAnnotations(AlignFrame alignFrame)
2204 boolean result = false;
2205 String param = applet.getParameter("annotations");
2208 param = setProtocolState(param);
2210 if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
2213 alignFrame.alignPanel.fontChanged();
2214 alignFrame.alignPanel.setScrollValues(0, 0);
2220 .println("Annotations were not added from annotation file '"
2228 * Load features file and view settings as specified by parameters. Returns
2229 * true if features were loaded, else false.
2234 protected boolean loadFeatures(AlignFrame alignFrame)
2236 boolean result = false;
2237 // ///////////////////////////
2238 // modify display of features
2239 // we do this before any features have been loaded, ensuring any hidden
2240 // groups are hidden when features first displayed
2242 // hide specific groups
2244 String param = applet.getParameter("hidefeaturegroups");
2247 alignFrame.setFeatureGroupState(separatorListToArray(param), false);
2248 // applet.setFeatureGroupStateOn(newAlignFrame, param, false);
2250 // show specific groups
2251 param = applet.getParameter("showfeaturegroups");
2254 alignFrame.setFeatureGroupState(separatorListToArray(param), true);
2255 // applet.setFeatureGroupStateOn(newAlignFrame, param, true);
2257 // and now load features
2258 param = applet.getParameter("features");
2261 param = setProtocolState(param);
2263 result = alignFrame.parseFeaturesFile(param, protocol);
2266 param = applet.getParameter("showFeatureSettings");
2267 if (param != null && param.equalsIgnoreCase(TRUE))
2269 alignFrame.viewport.setShowSequenceFeatures(true);
2270 new FeatureSettings(alignFrame.alignPanel);
2276 * Load a score file if specified by parameter. Returns true if file was
2277 * loaded, else false.
2281 protected boolean loadScoreFile(AlignFrame alignFrame)
2283 boolean result = false;
2284 String sScoreFile = applet.getParameter("scoreFile");
2285 if (sScoreFile != null && !"".equals(sScoreFile))
2292 .println("Attempting to load T-COFFEE score file from the scoreFile parameter");
2294 result = alignFrame.loadScoreFile(sScoreFile);
2298 .println("Failed to parse T-COFFEE parameter as a valid score file ('"
2299 + sScoreFile + "')");
2301 } catch (Exception e)
2303 System.err.printf("Cannot read score file: '%s'. Cause: %s \n",
2304 sScoreFile, e.getMessage());
2311 * Load a tree for the alignment if specified by parameter. Returns true if
2312 * a tree was loaded, else false.
2317 protected boolean loadTree(AlignFrame alignFrame)
2319 boolean result = false;
2320 String treeFile = applet.getParameter("tree");
2321 if (treeFile == null)
2323 treeFile = applet.getParameter("treeFile");
2326 if (treeFile != null)
2330 treeFile = setProtocolState(treeFile);
2331 NewickFile fin = new NewickFile(treeFile, protocol);
2334 if (fin.getTree() != null)
2336 alignFrame.loadTree(fin, treeFile);
2338 dbgMsg("Successfully imported tree.");
2342 dbgMsg("Tree parameter did not resolve to a valid tree.");
2344 } catch (Exception ex)
2346 ex.printStackTrace();
2353 * Discovers whether the given file is in the Applet Archive
2359 boolean inArchive(String file)
2361 // This might throw a security exception in certain browsers
2362 // Netscape Communicator for instance.
2365 boolean rtn = (getClass().getResourceAsStream("/" + file) != null);
2368 System.err.println("Resource '" + file + "' was "
2369 + (rtn ? "" : "not") + " located by classloader.");
2372 } catch (Exception ex)
2374 System.out.println("Exception checking resources: " + file + " "
2381 * If the file is not already in URL format, tries to locate it by resolving
2387 String addProtocol(final String f)
2389 if (f.indexOf("://") != -1)
2391 // already has URL format
2396 * Try relative to document base
2398 URL documentBase = getDocumentBase();
2399 String url = applet.resolveUrlForLocalOrAbsolute(f, documentBase);
2404 System.err.println("Prepended document base '" + documentBase
2405 + "' to make: '" + url + "'");
2411 * Try relative to codebase
2413 URL codeBase = getCodeBase();
2414 url = applet.resolveUrlForLocalOrAbsolute(f, codeBase);
2419 System.err.println("Prepended codebase '" + codeBase
2420 + "' to make: '" + url + "'");
2429 * Returns true if an input stream can be opened on the specified URL, else
2435 private boolean urlExists(String url)
2437 InputStream is = null;
2440 is = new URL(url).openStream();
2445 } catch (Exception x)
2455 } catch (IOException e)
2466 * @return the default alignFrame acted on by the public applet methods. May
2467 * return null with an error message on System.err indicating the
2470 public AlignFrame getDefaultTargetFrame()
2472 if (currentAlignFrame != null)
2474 return currentAlignFrame;
2476 if (initialAlignFrame != null)
2478 return initialAlignFrame;
2481 .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
2486 * separator used for separatorList
2488 protected String separator = "" + ((char) 0x00AC); // the default used to be
2489 // '|' but many sequence
2490 // IDS include pipes.
2493 * set to enable the URL based javascript execution mechanism
2495 public boolean jsfallbackEnabled = false;
2498 * parse the string into a list
2501 * @return elements separated by separator
2503 public String[] separatorListToArray(String list)
2505 return separatorListToArray(list, separator);
2509 * parse the string into a list
2513 * @return elements separated by separator
2515 public String[] separatorListToArray(String list, String separator)
2517 int seplen = separator.length();
2518 if (list == null || list.equals("") || list.equals(separator))
2522 java.util.Vector jv = new Vector();
2524 while ((pos = list.indexOf(separator, cp)) > cp)
2526 jv.addElement(list.substring(cp, pos));
2529 if (cp < list.length())
2531 String c = list.substring(cp);
2532 if (!c.equals(separator))
2539 String[] v = new String[jv.size()];
2540 for (int i = 0; i < v.length; i++)
2542 v[i] = (String) jv.elementAt(i);
2544 jv.removeAllElements();
2547 System.err.println("Array from '" + separator
2548 + "' separated List:\n" + v.length);
2549 for (int i = 0; i < v.length; i++)
2551 System.err.println("item " + i + " '" + v[i] + "'");
2558 System.err.println("Empty Array from '" + separator
2559 + "' separated List");
2565 * concatenate the list with separator
2568 * @return concatenated string
2570 public String arrayToSeparatorList(String[] list)
2572 return arrayToSeparatorList(list, separator);
2576 * concatenate the list with separator
2580 * @return concatenated string
2582 public String arrayToSeparatorList(String[] list, String separator)
2584 StringBuffer v = new StringBuffer();
2585 if (list != null && list.length > 0)
2587 for (int i = 0, iSize = list.length; i < iSize; i++)
2589 if (list[i] != null)
2593 v.append(separator);
2600 System.err.println("Returning '" + separator
2601 + "' separated List:\n");
2602 System.err.println(v);
2604 return v.toString();
2608 System.err.println("Returning empty '" + separator
2609 + "' separated List\n");
2611 return "" + separator;
2617 * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
2619 public String getFeatureGroups()
2621 String lst = arrayToSeparatorList(getDefaultTargetFrame()
2622 .getFeatureGroups());
2630 * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame
2633 public String getFeatureGroupsOn(AlignFrame alf)
2635 String lst = arrayToSeparatorList(alf.getFeatureGroups());
2642 * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)
2644 public String getFeatureGroupsOfState(boolean visible)
2646 return arrayToSeparatorList(getDefaultTargetFrame()
2647 .getFeatureGroupsOfState(visible));
2654 * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui
2655 * .AlignFrame, boolean)
2657 public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
2659 return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
2665 * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui.
2666 * AlignFrame, java.lang.String, boolean)
2668 public void setFeatureGroupStateOn(final AlignFrame alf,
2669 final String groups, boolean state)
2671 final boolean st = state;// !(state==null || state.equals("") ||
2672 // state.toLowerCase().equals("false"));
2673 java.awt.EventQueue.invokeLater(new Runnable()
2678 alf.setFeatureGroupState(separatorListToArray(groups), st);
2686 * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupState(java.lang.String,
2689 public void setFeatureGroupState(String groups, boolean state)
2691 setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
2697 * @see jalview.bin.JalviewLiteJsApi#getSeparator()
2699 public String getSeparator()
2707 * @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String)
2709 public void setSeparator(String separator)
2711 if (separator == null || separator.length() < 1)
2714 separator = "" + ((char) 0x00AC);
2716 this.separator = separator;
2719 System.err.println("Default Separator now: '" + separator + "'");
2724 * get boolean value of applet parameter 'name' and return default if
2725 * parameter is not set
2730 * the value to return otherwise
2731 * @return true or false
2733 public boolean getDefaultParameter(String name, boolean def)
2736 if ((stn = getParameter(name)) == null)
2740 if (TRUE.equalsIgnoreCase(stn))
2750 * @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame,
2751 * java.lang.String, java.lang.String, java.lang.String)
2753 public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
2754 String pdbEntryString, String pdbFile)
2756 return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);
2759 protected void setAlignPdbStructures(boolean alignPdbStructures)
2761 this.alignPdbStructures = alignPdbStructures;
2764 public boolean isAlignPdbStructures()
2766 return alignPdbStructures;
2771 // callInitCallback();
2774 private Hashtable<String, long[]> jshashes = new Hashtable<String, long[]>();
2776 private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<String, Hashtable<String, String[]>>();
2778 public void setJsMessageSet(String messageclass, String viewId,
2779 String[] colcommands)
2781 Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
2784 msgset = new Hashtable<String, String[]>();
2785 jsmessages.put(messageclass, msgset);
2787 msgset.put(viewId, colcommands);
2788 long[] l = new long[colcommands.length];
2789 for (int i = 0; i < colcommands.length; i++)
2791 l[i] = colcommands[i].hashCode();
2793 jshashes.put(messageclass + "|" + viewId, l);
2799 * @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String,
2802 public String getJsMessage(String messageclass, String viewId)
2804 Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
2807 String[] msgs = msgset.get(viewId);
2810 for (int i = 0; i < msgs.length; i++)
2812 if (msgs[i] != null)
2824 public boolean isJsMessageSetChanged(String string, String string2,
2825 String[] colcommands)
2827 long[] l = jshashes.get(string + "|" + string2);
2828 if (l == null && colcommands != null)
2832 for (int i = 0; i < colcommands.length; i++)
2834 if (l[i] != colcommands[i].hashCode())
2842 private Vector jsExecQueue = new Vector();
2844 public Vector getJsExecQueue()
2849 public void setExecutor(JSFunctionExec jsFunctionExec2)
2851 jsFunctionExec = jsFunctionExec2;
2855 * return the given colour value parameter or the given default if parameter
2862 public Color getDefaultColourParameter(String colparam, Color defcolour)
2864 String colprop = getParameter(colparam);
2865 if (colprop == null || colprop.trim().length() == 0)
2869 Color col = jalview.schemes.ColourSchemeProperty
2870 .getAWTColorFromName(colprop);
2875 col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
2876 } catch (Exception ex)
2878 System.err.println("Couldn't parse '" + colprop
2879 + "' as a colour for " + colparam);
2883 return (col == null) ? defcolour : col;
2887 public void openJalviewHelpUrl()
2889 String helpUrl = getParameter("jalviewhelpurl");
2890 if (helpUrl == null || helpUrl.trim().length() < 5)
2892 helpUrl = "http://www.jalview.org/help.html";
2894 showURL(helpUrl, "HELP");
2898 * form a complete URL given a path to a resource and a reference location on
2902 * - an absolute path on the same server as localref or a document
2903 * located relative to localref
2905 * - a URL on the same server as url
2906 * @return a complete URL for the resource located by url
2908 private String resolveUrlForLocalOrAbsolute(String url, URL localref)
2910 String codebase = localref.toString();
2911 if (url.indexOf("/") == 0)
2913 String localfile = localref.getFile();
2914 url = codebase.substring(0, codebase.length() - localfile.length())
2919 url = localref + url;
2923 System.err.println("URL: " + localref.toString());
2924 System.err.println("URL.getFile: " + localref.getFile());
2925 System.err.println("URL.getPath: " + localref.getPath());
2926 System.err.println("URL.getQuery: " + localref.getQuery());
2927 System.err.println("returning " + url);
2933 * open a URL in the browser - resolving it according to relative refs and
2934 * coping with javascript: protocol if necessary.
2939 public void showURL(String url, String target)
2943 if (url.indexOf(":") == -1)
2945 // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
2947 // Should really use docbase, not codebase.
2949 url = resolveUrlForLocalOrAbsolute(
2951 prepend = getDefaultParameter("resolvetocodebase", false) ? getDocumentBase()
2956 .println("Show url (prepended "
2958 + " - toggle resolvetocodebase if code/docbase resolution is wrong): "
2966 System.err.println("Show url: " + url);
2969 if (url.indexOf("javascript:") == 0)
2971 // no target for the javascript context
2972 getAppletContext().showDocument(new java.net.URL(url));
2976 getAppletContext().showDocument(new java.net.URL(url), target);
2978 } catch (Exception ex)
2980 ex.printStackTrace();
2985 * bind structures in a viewer to any matching sequences in an alignFrame (use
2986 * sequenceIds to limit scope of search to specific sequences)
2990 * @param sequenceIds
2991 * @return TODO: consider making an exception structure for indicating when
2992 * binding fails public SequenceStructureBinding
2993 * addStructureViewInstance( AlignFrame alFrame, Object viewer, String
2996 * if (sequenceIds != null && sequenceIds.length() > 0) { return
2997 * alFrame.addStructureViewInstance(viewer,
2998 * separatorListToArray(sequenceIds)); } else { return
2999 * alFrame.addStructureViewInstance(viewer, null); } // return null; }