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, String file2, JalviewLite _applet)
1814 this._file2 = file2;
1820 LoadJmolThread jmolchecker = new LoadJmolThread();
1821 jmolchecker.start();
1822 while (jmolchecker.notFinished())
1824 // wait around until the Jmol check is complete.
1828 } catch (Exception e)
1833 // applet.callInitCallback();
1837 * Load the alignment and any related files as specified by applet
1840 private void startLoading()
1842 dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");
1844 dbgMsg("Loading started.");
1846 AlignFrame newAlignFrame = readAlignment(_file);
1847 AlignFrame newAlignFrame2 = readAlignment(_file2);
1848 if (newAlignFrame != null)
1850 addToDisplay(newAlignFrame, newAlignFrame2);
1851 loadTree(newAlignFrame);
1853 loadScoreFile(newAlignFrame);
1855 loadFeatures(newAlignFrame);
1857 loadAnnotations(newAlignFrame);
1859 loadJnetFile(newAlignFrame);
1861 loadPdbFiles(newAlignFrame);
1866 applet.remove(launcher);
1873 * Add an AlignFrame to the display; or if two are provided, a SplitFrame.
1878 public void addToDisplay(AlignFrame af, AlignFrame af2)
1882 af.addToDisplay(embedded);
1886 SplitFrame sf = new SplitFrame(af, af2);
1887 sf.addToDisplay(embedded, JalviewLite.this);
1892 * Read the alignment file (from URL, text 'paste', or archive by
1897 protected AlignFrame readAlignment(String fileParam)
1899 if (fileParam == null)
1903 String resolvedFile = setProtocolState(fileParam);
1904 String format = new IdentifyFile().Identify(resolvedFile, protocol);
1905 dbgMsg("File identified as '" + format + "'");
1906 AlignmentI al = null;
1909 al = new AppletFormatAdapter().readFile(resolvedFile, protocol, format);
1910 if ((al != null) && (al.getHeight() > 0))
1912 dbgMsg("Successfully loaded file.");
1913 al.setDataset(null);
1914 AlignFrame newAlignFrame = new AlignFrame(al, applet,
1915 resolvedFile, embedded, false);
1916 newAlignFrame.setTitle(resolvedFile);
1917 if (initialAlignFrame == null)
1919 initialAlignFrame = newAlignFrame;
1921 // update the focus.
1922 currentAlignFrame = newAlignFrame;
1924 if (protocol == AppletFormatAdapter.PASTE)
1926 newAlignFrame.setTitle(MessageManager.formatMessage(
1927 "label.sequences_from", new Object[]
1928 { applet.getDocumentBase().toString() }));
1931 newAlignFrame.statusBar.setText(MessageManager.formatMessage(
1932 "label.successfully_loaded_file", new Object[]
1935 return newAlignFrame;
1937 } catch (java.io.IOException ex)
1939 dbgMsg("File load exception.");
1940 ex.printStackTrace();
1945 FileParse fp = new FileParse(resolvedFile, protocol);
1947 dbgMsg(">>>Dumping contents of '" + resolvedFile + "' " + "("
1949 while ((ln = fp.nextLine()) != null)
1953 dbgMsg(">>>Dump finished.");
1954 } catch (Exception e)
1957 .println("Exception when trying to dump the content of the file parameter.");
1958 e.printStackTrace();
1966 * Load PDBFiles if any specified by parameter(s). Returns true if loaded,
1972 protected boolean loadPdbFiles(AlignFrame alignFrame)
1974 boolean result = false;
1976 * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6 -
1977 * related to JAL-434
1980 applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",
1983 * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
1986 * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
1988 * <param name="PDBfile3" value="1q0o Q45135_9MICO">
1991 int pdbFileCount = 0;
1992 // Accumulate pdbs here if they are heading for the same view (if
1993 // alignPdbStructures is true)
1994 Vector pdbs = new Vector();
1995 // create a lazy matcher if we're asked to
1996 jalview.analysis.SequenceIdMatcher matcher = (applet
1997 .getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher(
1998 alignFrame.getAlignViewport().getAlignment()
1999 .getSequencesArray()) : null;
2004 if (pdbFileCount > 0)
2006 param = applet.getParameter("PDBFILE" + pdbFileCount);
2010 param = applet.getParameter("PDBFILE");
2015 PDBEntry pdb = new PDBEntry();
2018 SequenceI[] seqs = null;
2019 String[] chains = null;
2021 StringTokenizer st = new StringTokenizer(param, " ");
2023 if (st.countTokens() < 2)
2025 String sequence = applet.getParameter("PDBSEQ");
2026 if (sequence != null)
2028 seqs = new SequenceI[]
2029 { matcher == null ? (Sequence) alignFrame.getAlignViewport()
2030 .getAlignment().findName(sequence) : matcher
2031 .findIdMatch(sequence) };
2037 param = st.nextToken();
2038 Vector tmp = new Vector();
2039 Vector tmp2 = new Vector();
2041 while (st.hasMoreTokens())
2043 seqstring = st.nextToken();
2044 StringTokenizer st2 = new StringTokenizer(seqstring, "=");
2045 if (st2.countTokens() > 1)
2047 // This is the chain
2048 tmp2.addElement(st2.nextToken());
2049 seqstring = st2.nextToken();
2051 tmp.addElement(matcher == null ? (Sequence) alignFrame
2052 .getAlignViewport().getAlignment()
2053 .findName(seqstring) : matcher.findIdMatch(seqstring));
2056 seqs = new SequenceI[tmp.size()];
2058 if (tmp2.size() == tmp.size())
2060 chains = new String[tmp2.size()];
2061 tmp2.copyInto(chains);
2064 param = setProtocolState(param);
2066 if (// !jmolAvailable
2068 protocol == AppletFormatAdapter.CLASSLOADER && !useXtrnalSviewer)
2070 // Re: JAL-357 : the bug isn't a problem if we are using an
2072 // TODO: verify this Re:
2073 // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
2074 // This exception preserves the current behaviour where, even if
2075 // the local pdb file was identified in the class loader
2076 protocol = AppletFormatAdapter.URL; // this is probably NOT
2078 param = addProtocol(param); //
2085 for (int i = 0; i < seqs.length; i++)
2087 if (seqs[i] != null)
2089 ((Sequence) seqs[i]).addPDBId(pdb);
2090 StructureSelectionManager.getStructureSelectionManager(
2091 applet).registerPDBEntry(pdb);
2095 if (JalviewLite.debug)
2097 // this may not really be a problem but we give a warning
2100 .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
2106 if (!alignPdbStructures)
2108 alignFrame.newStructureView(applet, pdb, seqs, chains,
2113 pdbs.addElement(new Object[]
2114 { pdb, seqs, chains, new String(protocol) });
2120 } while (param != null || pdbFileCount < 10);
2121 if (pdbs.size() > 0)
2123 SequenceI[][] seqs = new SequenceI[pdbs.size()][];
2124 PDBEntry[] pdb = new PDBEntry[pdbs.size()];
2125 String[][] chains = new String[pdbs.size()][];
2126 String[] protocols = new String[pdbs.size()];
2127 for (int pdbsi = 0, pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)
2129 Object[] o = (Object[]) pdbs.elementAt(pdbsi);
2130 pdb[pdbsi] = (PDBEntry) o[0];
2131 seqs[pdbsi] = (SequenceI[]) o[1];
2132 chains[pdbsi] = (String[]) o[2];
2133 protocols[pdbsi] = (String) o[3];
2135 alignFrame.alignedStructureView(applet, pdb, seqs, chains,
2143 * Load in a Jnetfile if specified by parameter. Returns true if loaded,
2149 protected boolean loadJnetFile(AlignFrame alignFrame)
2151 boolean result = false;
2152 String param = applet.getParameter("jnetfile");
2157 param = setProtocolState(param);
2158 JPredFile predictions = new JPredFile(param, protocol);
2159 JnetAnnotationMaker.add_annotation(predictions,
2160 alignFrame.viewport.getAlignment(), 0, false);
2161 // false == do not add sequence profile from concise output
2162 SequenceI repseq = alignFrame.viewport.getAlignment()
2164 alignFrame.viewport.getAlignment().setSeqrep(repseq);
2165 ColumnSelection cs = new ColumnSelection();
2166 cs.hideInsertionsFor(repseq);
2167 alignFrame.viewport.setColumnSelection(cs);
2168 alignFrame.alignPanel.fontChanged();
2169 alignFrame.alignPanel.setScrollValues(0, 0);
2171 } catch (Exception ex)
2173 ex.printStackTrace();
2180 * Load annotations if specified by parameter. Returns true if loaded, else
2186 protected boolean loadAnnotations(AlignFrame alignFrame)
2188 boolean result = false;
2189 String param = applet.getParameter("annotations");
2192 param = setProtocolState(param);
2194 if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
2197 alignFrame.alignPanel.fontChanged();
2198 alignFrame.alignPanel.setScrollValues(0, 0);
2204 .println("Annotations were not added from annotation file '"
2212 * Load features file and view settings as specified by parameters. Returns
2213 * true if features were loaded, else false.
2218 protected boolean loadFeatures(AlignFrame alignFrame)
2220 boolean result = false;
2221 // ///////////////////////////
2222 // modify display of features
2223 // we do this before any features have been loaded, ensuring any hidden
2224 // groups are hidden when features first displayed
2226 // hide specific groups
2228 String param = applet.getParameter("hidefeaturegroups");
2231 alignFrame.setFeatureGroupState(separatorListToArray(param), false);
2232 // applet.setFeatureGroupStateOn(newAlignFrame, param, false);
2234 // show specific groups
2235 param = applet.getParameter("showfeaturegroups");
2238 alignFrame.setFeatureGroupState(separatorListToArray(param), true);
2239 // applet.setFeatureGroupStateOn(newAlignFrame, param, true);
2241 // and now load features
2242 param = applet.getParameter("features");
2245 param = setProtocolState(param);
2247 result = alignFrame.parseFeaturesFile(param, protocol);
2250 param = applet.getParameter("showFeatureSettings");
2251 if (param != null && param.equalsIgnoreCase(TRUE))
2253 alignFrame.viewport.setShowSequenceFeatures(true);
2254 new FeatureSettings(alignFrame.alignPanel);
2260 * Load a score file if specified by parameter. Returns true if file was
2261 * loaded, else false.
2265 protected boolean loadScoreFile(AlignFrame alignFrame)
2267 boolean result = false;
2268 String sScoreFile = applet.getParameter("scoreFile");
2269 if (sScoreFile != null && !"".equals(sScoreFile))
2276 .println("Attempting to load T-COFFEE score file from the scoreFile parameter");
2278 result = alignFrame.loadScoreFile(sScoreFile);
2282 .println("Failed to parse T-COFFEE parameter as a valid score file ('"
2283 + sScoreFile + "')");
2285 } catch (Exception e)
2287 System.err.printf("Cannot read score file: '%s'. Cause: %s \n",
2288 sScoreFile, e.getMessage());
2295 * Load a tree for the alignment if specified by parameter. Returns true if
2296 * a tree was loaded, else false.
2301 protected boolean loadTree(AlignFrame alignFrame)
2303 boolean result = false;
2304 String treeFile = applet.getParameter("tree");
2305 if (treeFile == null)
2307 treeFile = applet.getParameter("treeFile");
2310 if (treeFile != null)
2314 treeFile = setProtocolState(treeFile);
2315 NewickFile fin = new NewickFile(treeFile, protocol);
2318 if (fin.getTree() != null)
2320 alignFrame.loadTree(fin, treeFile);
2322 dbgMsg("Successfully imported tree.");
2326 dbgMsg("Tree parameter did not resolve to a valid tree.");
2328 } catch (Exception ex)
2330 ex.printStackTrace();
2337 * Discovers whether the given file is in the Applet Archive
2343 boolean inArchive(String file)
2345 // This might throw a security exception in certain browsers
2346 // Netscape Communicator for instance.
2349 boolean rtn = (getClass().getResourceAsStream("/" + file) != null);
2352 System.err.println("Resource '" + file + "' was "
2353 + (rtn ? "" : "not") + " located by classloader.");
2356 } catch (Exception ex)
2358 System.out.println("Exception checking resources: " + file + " "
2365 * If the file is not already in URL format, tries to locate it by resolving
2371 String addProtocol(final String file)
2373 if (file.indexOf("://") == -1)
2376 * Try relative to document base
2378 String url = applet.resolveUrlForLocalOrAbsolute(file,
2384 System.err.println("Prepended document base for resource: '"
2391 * Try relative to codebase
2393 url = applet.resolveUrlForLocalOrAbsolute(file, getCodeBase());
2398 System.err.println("Prepended codebase for resource: '" + file
2406 * Not resolved, leave unchanged
2412 * Returns true if an input stream can be opened on the specified URL, else
2418 private boolean urlExists(String url)
2420 InputStream is = null;
2423 is = new URL(url).openStream();
2428 } catch (Exception x)
2438 } catch (IOException e)
2449 * @return the default alignFrame acted on by the public applet methods. May
2450 * return null with an error message on System.err indicating the
2453 public AlignFrame getDefaultTargetFrame()
2455 if (currentAlignFrame != null)
2457 return currentAlignFrame;
2459 if (initialAlignFrame != null)
2461 return initialAlignFrame;
2464 .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
2469 * separator used for separatorList
2471 protected String separator = "" + ((char) 0x00AC); // the default used to be
2472 // '|' but many sequence
2473 // IDS include pipes.
2476 * set to enable the URL based javascript execution mechanism
2478 public boolean jsfallbackEnabled = false;
2481 * parse the string into a list
2484 * @return elements separated by separator
2486 public String[] separatorListToArray(String list)
2488 return separatorListToArray(list, separator);
2492 * parse the string into a list
2496 * @return elements separated by separator
2498 public String[] separatorListToArray(String list, String separator)
2500 // note separator local variable intentionally masks object field
2501 int seplen = separator.length();
2502 if (list == null || list.equals("") || list.equals(separator))
2506 java.util.Vector jv = new Vector();
2508 while ((pos = list.indexOf(separator, cp)) > cp)
2510 jv.addElement(list.substring(cp, pos));
2513 if (cp < list.length())
2515 String c = list.substring(cp);
2516 if (!c.equals(separator))
2523 String[] v = new String[jv.size()];
2524 for (int i = 0; i < v.length; i++)
2526 v[i] = (String) jv.elementAt(i);
2528 jv.removeAllElements();
2531 System.err.println("Array from '" + separator
2532 + "' separated List:\n" + v.length);
2533 for (int i = 0; i < v.length; i++)
2535 System.err.println("item " + i + " '" + v[i] + "'");
2542 System.err.println("Empty Array from '" + separator
2543 + "' separated List");
2549 * concatenate the list with separator
2552 * @return concatenated string
2554 public String arrayToSeparatorList(String[] list)
2556 return arrayToSeparatorList(list, separator);
2560 * concatenate the list with separator
2564 * @return concatenated string
2566 public String arrayToSeparatorList(String[] list, String separator)
2568 StringBuffer v = new StringBuffer();
2569 if (list != null && list.length > 0)
2571 for (int i = 0, iSize = list.length; i < iSize; i++)
2573 if (list[i] != null)
2577 v.append(separator);
2584 System.err.println("Returning '" + separator
2585 + "' separated List:\n");
2586 System.err.println(v);
2588 return v.toString();
2592 System.err.println("Returning empty '" + separator
2593 + "' separated List\n");
2595 return "" + separator;
2601 * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
2603 public String getFeatureGroups()
2605 String lst = arrayToSeparatorList(getDefaultTargetFrame()
2606 .getFeatureGroups());
2614 * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame
2617 public String getFeatureGroupsOn(AlignFrame alf)
2619 String lst = arrayToSeparatorList(alf.getFeatureGroups());
2626 * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)
2628 public String getFeatureGroupsOfState(boolean visible)
2630 return arrayToSeparatorList(getDefaultTargetFrame()
2631 .getFeatureGroupsOfState(visible));
2638 * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui
2639 * .AlignFrame, boolean)
2641 public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
2643 return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
2649 * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui.
2650 * AlignFrame, java.lang.String, boolean)
2652 public void setFeatureGroupStateOn(final AlignFrame alf,
2653 final String groups, boolean state)
2655 final boolean st = state;// !(state==null || state.equals("") ||
2656 // state.toLowerCase().equals("false"));
2657 java.awt.EventQueue.invokeLater(new Runnable()
2662 alf.setFeatureGroupState(separatorListToArray(groups), st);
2670 * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupState(java.lang.String,
2673 public void setFeatureGroupState(String groups, boolean state)
2675 setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
2681 * @see jalview.bin.JalviewLiteJsApi#getSeparator()
2683 public String getSeparator()
2691 * @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String)
2693 public void setSeparator(String separator)
2695 if (separator == null || separator.length() < 1)
2698 separator = "" + ((char) 0x00AC);
2700 this.separator = separator;
2703 System.err.println("Default Separator now: '" + separator + "'");
2708 * get boolean value of applet parameter 'name' and return default if
2709 * parameter is not set
2714 * the value to return otherwise
2715 * @return true or false
2717 public boolean getDefaultParameter(String name, boolean def)
2720 if ((stn = getParameter(name)) == null)
2724 if (stn.toLowerCase().equals(TRUE))
2734 * @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame,
2735 * java.lang.String, java.lang.String, java.lang.String)
2737 public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
2738 String pdbEntryString, String pdbFile)
2740 return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);
2743 protected void setAlignPdbStructures(boolean alignPdbStructures)
2745 this.alignPdbStructures = alignPdbStructures;
2748 public boolean isAlignPdbStructures()
2750 return alignPdbStructures;
2755 // callInitCallback();
2758 private Hashtable<String, long[]> jshashes = new Hashtable<String, long[]>();
2760 private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<String, Hashtable<String, String[]>>();
2762 public void setJsMessageSet(String messageclass, String viewId,
2763 String[] colcommands)
2765 Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
2768 msgset = new Hashtable<String, String[]>();
2769 jsmessages.put(messageclass, msgset);
2771 msgset.put(viewId, colcommands);
2772 long[] l = new long[colcommands.length];
2773 for (int i = 0; i < colcommands.length; i++)
2775 l[i] = colcommands[i].hashCode();
2777 jshashes.put(messageclass + "|" + viewId, l);
2783 * @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String,
2786 public String getJsMessage(String messageclass, String viewId)
2788 Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
2791 String[] msgs = msgset.get(viewId);
2794 for (int i = 0; i < msgs.length; i++)
2796 if (msgs[i] != null)
2808 public boolean isJsMessageSetChanged(String string, String string2,
2809 String[] colcommands)
2811 long[] l = jshashes.get(string + "|" + string2);
2812 if (l == null && colcommands != null)
2816 for (int i = 0; i < colcommands.length; i++)
2818 if (l[i] != colcommands[i].hashCode())
2826 private Vector jsExecQueue = new Vector();
2828 public Vector getJsExecQueue()
2833 public void setExecutor(JSFunctionExec jsFunctionExec2)
2835 jsFunctionExec = jsFunctionExec2;
2839 * return the given colour value parameter or the given default if parameter
2846 public Color getDefaultColourParameter(String colparam, Color defcolour)
2848 String colprop = getParameter(colparam);
2849 if (colprop == null || colprop.trim().length() == 0)
2853 Color col = jalview.schemes.ColourSchemeProperty
2854 .getAWTColorFromName(colprop);
2859 col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
2860 } catch (Exception ex)
2862 System.err.println("Couldn't parse '" + colprop
2863 + "' as a colour for " + colparam);
2867 return (col == null) ? defcolour : col;
2871 public void openJalviewHelpUrl()
2873 String helpUrl = getParameter("jalviewhelpurl");
2874 if (helpUrl == null || helpUrl.trim().length() < 5)
2876 helpUrl = "http://www.jalview.org/help.html";
2878 showURL(helpUrl, "HELP");
2882 * form a complete URL given a path to a resource and a reference location on
2886 * - an absolute path on the same server as localref or a document
2887 * located relative to localref
2889 * - a URL on the same server as url
2890 * @return a complete URL for the resource located by url
2892 private String resolveUrlForLocalOrAbsolute(String url, URL localref)
2894 String codebase = localref.toString();
2895 if (url.indexOf("/") == 0)
2897 url = codebase.substring(0, codebase.length()
2898 - localref.getFile().length())
2903 url = localref + url;
2909 * open a URL in the browser - resolving it according to relative refs and
2910 * coping with javascript: protocol if necessary.
2915 public void showURL(String url, String target)
2919 if (url.indexOf(":") == -1)
2921 // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
2923 // Should really use docbase, not codebase.
2925 url = resolveUrlForLocalOrAbsolute(
2927 prepend = getDefaultParameter("resolvetocodebase", false) ? getDocumentBase()
2932 .println("Show url (prepended "
2934 + " - toggle resolvetocodebase if code/docbase resolution is wrong): "
2942 System.err.println("Show url: " + url);
2945 if (url.indexOf("javascript:") == 0)
2947 // no target for the javascript context
2948 getAppletContext().showDocument(new java.net.URL(url));
2952 getAppletContext().showDocument(new java.net.URL(url), target);
2954 } catch (Exception ex)
2956 ex.printStackTrace();
2961 * bind structures in a viewer to any matching sequences in an alignFrame (use
2962 * sequenceIds to limit scope of search to specific sequences)
2966 * @param sequenceIds
2967 * @return TODO: consider making an exception structure for indicating when
2968 * binding fails public SequenceStructureBinding
2969 * addStructureViewInstance( AlignFrame alFrame, Object viewer, String
2972 * if (sequenceIds != null && sequenceIds.length() > 0) { return
2973 * alFrame.addStructureViewInstance(viewer,
2974 * separatorListToArray(sequenceIds)); } else { return
2975 * alFrame.addStructureViewInstance(viewer, null); } // return null; }