2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 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.datamodel.Alignment;
29 import jalview.datamodel.AlignmentI;
30 import jalview.datamodel.AlignmentOrder;
31 import jalview.datamodel.ColumnSelection;
32 import jalview.datamodel.PDBEntry;
33 import jalview.datamodel.Sequence;
34 import jalview.datamodel.SequenceGroup;
35 import jalview.datamodel.SequenceI;
36 import jalview.io.AnnotationFile;
37 import jalview.io.AppletFormatAdapter;
38 import jalview.io.FileParse;
39 import jalview.io.IdentifyFile;
40 import jalview.io.JnetAnnotationMaker;
41 import jalview.javascript.JSFunctionExec;
42 import jalview.javascript.JalviewLiteJsApi;
43 import jalview.javascript.JsCallBack;
44 import jalview.structure.SelectionListener;
45 import jalview.structure.StructureSelectionManager;
46 import jalview.util.MessageManager;
48 import java.applet.Applet;
49 import java.awt.Button;
50 import java.awt.Color;
51 import java.awt.Component;
52 import java.awt.EventQueue;
54 import java.awt.Frame;
55 import java.awt.Graphics;
56 import java.awt.event.ActionEvent;
57 import java.awt.event.WindowAdapter;
58 import java.awt.event.WindowEvent;
59 import java.io.BufferedReader;
60 import java.io.InputStreamReader;
62 import java.util.Hashtable;
63 import java.util.List;
64 import java.util.StringTokenizer;
65 import java.util.Vector;
67 import netscape.javascript.JSException;
68 import netscape.javascript.JSObject;
71 * Jalview Applet. Runs in Java 1.18 runtime
74 * @version $Revision: 1.92 $
76 public class JalviewLite extends Applet implements
77 StructureSelectionManagerProvider, JalviewLiteJsApi
80 public StructureSelectionManager getStructureSelectionManager()
82 return StructureSelectionManager.getStructureSelectionManager(this);
85 // /////////////////////////////////////////
86 // The following public methods maybe called
87 // externally, eg via javascript in HTML page
91 * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences()
93 public String getSelectedSequences()
95 return getSelectedSequencesFrom(getDefaultTargetFrame());
101 * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
103 public String getSelectedSequences(String sep)
105 return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);
112 * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
115 public String getSelectedSequencesFrom(AlignFrame alf)
117 return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);
124 * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
125 * .AlignFrame, java.lang.String)
127 public String getSelectedSequencesFrom(AlignFrame alf, String sep)
129 StringBuffer result = new StringBuffer("");
130 if (sep == null || sep.length() == 0)
132 sep = separator; // "+0x00AC;
134 if (alf.viewport.getSelectionGroup() != null)
136 SequenceI[] seqs = alf.viewport.getSelectionGroup()
137 .getSequencesInOrder(alf.viewport.getAlignment());
139 for (int i = 0; i < seqs.length; i++)
141 result.append(seqs[i].getName());
146 return result.toString();
152 * @see jalview.bin.JalviewLiteJsApi#highlight(java.lang.String,
153 * java.lang.String, java.lang.String)
155 public void highlight(String sequenceId, String position,
156 String alignedPosition)
158 highlightIn(getDefaultTargetFrame(), sequenceId, position,
165 * @see jalview.bin.JalviewLiteJsApi#highlightIn(jalview.appletgui.AlignFrame,
166 * java.lang.String, java.lang.String, java.lang.String)
168 public void highlightIn(final AlignFrame alf, final String sequenceId,
169 final String position, final String alignedPosition)
171 // TODO: could try to highlight in all alignments if alf==null
172 jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
173 alf.viewport.getAlignment().getSequencesArray());
174 final SequenceI sq = matcher.findIdMatch(sequenceId);
180 apos = new Integer(position).intValue();
182 } catch (NumberFormatException ex)
186 final StructureSelectionManagerProvider me = this;
187 final int pos = apos;
188 // use vamsas listener to broadcast to all listeners in scope
189 if (alignedPosition != null
190 && (alignedPosition.trim().length() == 0 || alignedPosition
191 .toLowerCase().indexOf("false") > -1))
193 java.awt.EventQueue.invokeLater(new Runnable()
198 StructureSelectionManager.getStructureSelectionManager(me)
199 .mouseOverVamsasSequence(sq, sq.findIndex(pos), null);
205 java.awt.EventQueue.invokeLater(new Runnable()
210 StructureSelectionManager.getStructureSelectionManager(me)
211 .mouseOverVamsasSequence(sq, pos, null);
221 * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
224 public void select(String sequenceIds, String columns)
226 selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator);
232 * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
233 * java.lang.String, java.lang.String)
235 public void select(String sequenceIds, String columns, String sep)
237 selectIn(getDefaultTargetFrame(), sequenceIds, columns, sep);
243 * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
244 * java.lang.String, java.lang.String)
246 public void selectIn(AlignFrame alf, String sequenceIds, String columns)
248 selectIn(alf, sequenceIds, columns, separator);
254 * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
255 * java.lang.String, java.lang.String, java.lang.String)
257 public void selectIn(final AlignFrame alf, String sequenceIds,
258 String columns, String sep)
260 if (sep == null || sep.length() == 0)
268 System.err.println("Selecting region using separator string '"
273 String[] ids = separatorListToArray(sequenceIds, sep);
274 String[] cols = separatorListToArray(columns, sep);
275 final SequenceGroup sel = new SequenceGroup();
276 final ColumnSelection csel = new ColumnSelection();
277 AlignmentI al = alf.viewport.getAlignment();
278 jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
279 alf.viewport.getAlignment().getSequencesArray());
280 int start = 0, end = al.getWidth(), alw = al.getWidth();
281 boolean seqsfound = true;
282 if (ids != null && ids.length > 0)
285 for (int i = 0; i < ids.length; i++)
287 if (ids[i].trim().length() == 0)
291 SequenceI sq = matcher.findIdMatch(ids[i]);
295 sel.addSequence(sq, false);
299 boolean inseqpos = false;
300 if (cols != null && cols.length > 0)
302 boolean seset = false;
303 for (int i = 0; i < cols.length; i++)
305 String cl = cols[i].trim();
306 if (cl.length() == 0)
311 if ((p = cl.indexOf("-")) > -1)
313 int from = -1, to = -1;
316 from = new Integer(cl.substring(0, p)).intValue();
318 } catch (NumberFormatException ex)
321 .println("ERROR: Couldn't parse first integer in range element column selection string '"
322 + cl + "' - format is 'from-to'");
327 to = new Integer(cl.substring(p + 1)).intValue();
329 } catch (NumberFormatException ex)
332 .println("ERROR: Couldn't parse second integer in range element column selection string '"
333 + cl + "' - format is 'from-to'");
336 if (from >= 0 && to >= 0)
353 // comment to prevent range extension
363 for (int r = from; r <= to; r++)
365 if (r >= 0 && r < alw)
372 System.err.println("Range '" + cl + "' deparsed as [" + from
378 System.err.println("ERROR: Invalid Range '" + cl
379 + "' deparsed as [" + from + "," + to + "]");
387 r = new Integer(cl).intValue();
389 } catch (NumberFormatException ex)
391 if (cl.toLowerCase().equals("sequence"))
393 // we are in the dataset sequence's coordinate frame.
399 .println("ERROR: Couldn't parse integer from point selection element of column selection string '"
404 if (r >= 0 && r <= alw)
414 // comment to prevent range extension
427 System.err.println("Point selection '" + cl
428 + "' deparsed as [" + r + "]");
433 System.err.println("ERROR: Invalid Point selection '" + cl
434 + "' deparsed as [" + r + "]");
441 // we only propagate the selection when it was the null selection, or the
442 // given sequences were found in the alignment.
443 if (inseqpos && sel.getSize() > 0)
445 // assume first sequence provides reference frame ?
446 SequenceI rs = sel.getSequenceAt(0);
447 start = rs.findIndex(start);
448 end = rs.findIndex(end);
451 List<Integer> cs = csel.getSelected();
453 for (Integer selectedCol : cs)
455 csel.addElement(rs.findIndex(selectedCol));
459 sel.setStartRes(start);
461 EventQueue.invokeLater(new Runnable()
466 alf.select(sel, csel);
476 * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignment(java.lang.
477 * String, java.lang.String)
479 public String getSelectedSequencesAsAlignment(String format, String suffix)
481 return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(),
489 * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignmentFrom(jalview
490 * .appletgui.AlignFrame, java.lang.String, java.lang.String)
492 public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
493 String format, String suffix)
497 boolean seqlimits = suffix.equalsIgnoreCase("true");
498 if (alf.viewport.getSelectionGroup() != null)
500 // JBPNote: getSelectionAsNewSequence behaviour has changed - this
501 // method now returns a full copy of sequence data
502 // TODO consider using getSequenceSelection instead here
503 String reply = new AppletFormatAdapter().formatSequences(format,
504 new Alignment(alf.viewport.getSelectionAsNewSequence()),
508 } catch (Exception ex)
510 ex.printStackTrace();
511 return "Error retrieving alignment in " + format + " format. ";
519 * @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder()
521 public String getAlignmentOrder()
523 return getAlignmentOrderFrom(getDefaultTargetFrame());
530 * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
533 public String getAlignmentOrderFrom(AlignFrame alf)
535 return getAlignmentOrderFrom(alf, separator);
542 * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
543 * , java.lang.String)
545 public String getAlignmentOrderFrom(AlignFrame alf, String sep)
547 AlignmentI alorder = alf.getAlignViewport().getAlignment();
548 String[] order = new String[alorder.getHeight()];
549 for (int i = 0; i < order.length; i++)
551 order[i] = alorder.getSequenceAt(i).getName();
553 return arrayToSeparatorList(order);
559 * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
562 public String orderBy(String order, String undoName)
564 return orderBy(order, undoName, separator);
570 * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
571 * java.lang.String, java.lang.String)
573 public String orderBy(String order, String undoName, String sep)
575 return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep);
582 * jalview.bin.JalviewLiteJsApi#orderAlignmentBy(jalview.appletgui.AlignFrame,
583 * java.lang.String, java.lang.String, java.lang.String)
585 public String orderAlignmentBy(AlignFrame alf, String order,
586 String undoName, String sep)
588 String[] ids = separatorListToArray(order, sep);
589 SequenceI[] sqs = null;
590 if (ids != null && ids.length > 0)
592 jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
593 alf.viewport.getAlignment().getSequencesArray());
595 sqs = new SequenceI[ids.length];
596 for (int i = 0; i < ids.length; i++)
598 if (ids[i].trim().length() == 0)
602 SequenceI sq = matcher.findIdMatch(ids[i]);
610 SequenceI[] sqq = new SequenceI[s];
611 System.arraycopy(sqs, 0, sqq, 0, s);
624 final AlignmentOrder aorder = new AlignmentOrder(sqs);
626 if (undoName != null && undoName.trim().length() == 0)
630 final String _undoName = undoName;
631 // TODO: deal with synchronization here: cannot raise any events until after
632 // this has returned.
633 return alf.sortBy(aorder, _undoName) ? "true" : "";
639 * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String)
641 public String getAlignment(String format)
643 return getAlignmentFrom(getDefaultTargetFrame(), format, "true");
650 * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
653 public String getAlignmentFrom(AlignFrame alf, String format)
655 return getAlignmentFrom(alf, format, "true");
661 * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String,
664 public String getAlignment(String format, String suffix)
666 return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);
673 * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
674 * java.lang.String, java.lang.String)
676 public String getAlignmentFrom(AlignFrame alf, String format,
681 boolean seqlimits = suffix.equalsIgnoreCase("true");
683 String reply = new AppletFormatAdapter().formatSequences(format,
684 alf.viewport.getAlignment(), seqlimits);
686 } catch (Exception ex)
688 ex.printStackTrace();
689 return "Error retrieving alignment in " + format + " format. ";
696 * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
698 public void loadAnnotation(String annotation)
700 loadAnnotationFrom(getDefaultTargetFrame(), annotation);
707 * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
708 * , java.lang.String)
710 public void loadAnnotationFrom(AlignFrame alf, String annotation)
712 if (new AnnotationFile().readAnnotationFile(alf.getAlignViewport()
713 .getAlignment(), annotation, AppletFormatAdapter.PASTE))
715 alf.alignPanel.fontChanged();
716 alf.alignPanel.setScrollValues(0, 0);
720 alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
727 * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
729 public void loadFeatures(String features, boolean autoenabledisplay)
731 loadFeaturesFrom(getDefaultTargetFrame(), features, autoenabledisplay);
738 * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
739 * , java.lang.String)
741 public boolean loadFeaturesFrom(AlignFrame alf, String features,
742 boolean autoenabledisplay)
744 return alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE,
751 * @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String)
753 public String getFeatures(String format)
755 return getFeaturesFrom(getDefaultTargetFrame(), format);
762 * jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame,
765 public String getFeaturesFrom(AlignFrame alf, String format)
767 return alf.outputFeatures(false, format);
773 * @see jalview.bin.JalviewLiteJsApi#getAnnotation()
775 public String getAnnotation()
777 return getAnnotationFrom(getDefaultTargetFrame());
784 * jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame
787 public String getAnnotationFrom(AlignFrame alf)
789 return alf.outputAnnotations(false);
795 * @see jalview.bin.JalviewLiteJsApi#newView()
797 public AlignFrame newView()
799 return newViewFrom(getDefaultTargetFrame());
805 * @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String)
807 public AlignFrame newView(String name)
809 return newViewFrom(getDefaultTargetFrame(), name);
815 * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame)
817 public AlignFrame newViewFrom(AlignFrame alf)
819 return alf.newView(null);
825 * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame,
828 public AlignFrame newViewFrom(AlignFrame alf, String name)
830 return alf.newView(name);
836 * @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String,
839 public AlignFrame loadAlignment(String text, String title)
843 String format = new IdentifyFile().Identify(text,
844 AppletFormatAdapter.PASTE);
847 al = new AppletFormatAdapter().readFile(text,
848 AppletFormatAdapter.PASTE, format);
849 if (al.getHeight() > 0)
851 return new AlignFrame(al, this, title, false);
853 } catch (java.io.IOException ex)
855 ex.printStackTrace();
863 * @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String)
865 public void setMouseoverListener(String listener)
867 setMouseoverListener(currentAlignFrame, listener);
870 private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<jalview.javascript.JSFunctionExec>();
876 * jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame
877 * , java.lang.String)
879 public void setMouseoverListener(AlignFrame af, String listener)
881 if (listener != null)
883 listener = listener.trim();
884 if (listener.length() == 0)
887 .println("jalview Javascript error: Ignoring empty function for mouseover listener.");
891 jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener(
893 javascriptListeners.addElement(mol);
894 StructureSelectionManager.getStructureSelectionManager(this)
895 .addStructureViewerListener(mol);
898 System.err.println("Added a mouseover listener for "
899 + ((af == null) ? "All frames" : "Just views for "
900 + af.getAlignViewport().getSequenceSetId()));
901 System.err.println("There are now " + javascriptListeners.size()
902 + " listeners in total.");
909 * @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String)
911 public void setSelectionListener(String listener)
913 setSelectionListener(null, listener);
920 * jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame
921 * , java.lang.String)
923 public void setSelectionListener(AlignFrame af, String listener)
925 if (listener != null)
927 listener = listener.trim();
928 if (listener.length() == 0)
931 .println("jalview Javascript error: Ignoring empty function for selection listener.");
935 jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender(
937 javascriptListeners.addElement(mol);
938 StructureSelectionManager.getStructureSelectionManager(this)
939 .addSelectionListener(mol);
942 System.err.println("Added a selection listener for "
943 + ((af == null) ? "All frames" : "Just views for "
944 + af.getAlignViewport().getSequenceSetId()));
945 System.err.println("There are now " + javascriptListeners.size()
946 + " listeners in total.");
953 * @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String,
956 public void setStructureListener(String listener, String modelSet)
958 if (listener != null)
960 listener = listener.trim();
961 if (listener.length() == 0)
964 .println("jalview Javascript error: Ignoring empty function for selection listener.");
968 jalview.javascript.MouseOverStructureListener mol = new jalview.javascript.MouseOverStructureListener(
969 this, listener, separatorListToArray(modelSet));
970 javascriptListeners.addElement(mol);
971 StructureSelectionManager.getStructureSelectionManager(this)
972 .addStructureViewerListener(mol);
975 System.err.println("Added a javascript structure viewer listener '"
977 System.err.println("There are now " + javascriptListeners.size()
978 + " listeners in total.");
986 * jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui
987 * .AlignFrame, java.lang.String)
989 public void removeJavascriptListener(AlignFrame af, String listener)
991 if (listener != null)
993 listener = listener.trim();
994 if (listener.length() == 0)
999 boolean rprt = false;
1000 for (int ms = 0, msSize = javascriptListeners.size(); ms < msSize;)
1002 Object lstn = javascriptListeners.elementAt(ms);
1003 JsCallBack lstner = (JsCallBack) lstn;
1004 if ((af == null || lstner.getAlignFrame() == af)
1005 && (listener == null || lstner.getListenerFunction().equals(
1008 javascriptListeners.removeElement(lstner);
1010 if (lstner instanceof SelectionListener)
1012 StructureSelectionManager.getStructureSelectionManager(this)
1013 .removeSelectionListener((SelectionListener) lstner);
1017 StructureSelectionManager.getStructureSelectionManager(this)
1018 .removeStructureViewerListener(lstner, null);
1023 System.err.println("Removed listener '" + listener + "'");
1033 System.err.println("There are now " + javascriptListeners.size()
1034 + " listeners in total.");
1040 System.err.println("Applet " + getName() + " stop().");
1044 public void destroy()
1046 System.err.println("Applet " + getName() + " destroy().");
1050 private void tidyUp()
1053 if (currentAlignFrame != null && currentAlignFrame.viewport != null
1054 && currentAlignFrame.viewport.applet != null)
1056 AlignViewport av = currentAlignFrame.viewport;
1057 currentAlignFrame.closeMenuItem_actionPerformed();
1059 currentAlignFrame = null;
1061 if (javascriptListeners != null)
1063 while (javascriptListeners.size() > 0)
1065 jalview.javascript.JSFunctionExec mol = javascriptListeners
1067 javascriptListeners.removeElement(mol);
1068 if (mol instanceof SelectionListener)
1070 StructureSelectionManager.getStructureSelectionManager(this)
1071 .removeSelectionListener((SelectionListener) mol);
1075 StructureSelectionManager.getStructureSelectionManager(this)
1076 .removeStructureViewerListener(mol, null);
1081 if (jsFunctionExec != null)
1083 jsFunctionExec.stopQueue();
1084 jsFunctionExec.jvlite = null;
1086 initialAlignFrame = null;
1087 jsFunctionExec = null;
1088 javascriptListeners = null;
1089 StructureSelectionManager.release(this);
1092 private jalview.javascript.JSFunctionExec jsFunctionExec;
1097 * @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String,
1098 * java.lang.String, java.lang.String)
1100 public void mouseOverStructure(final String pdbResNum,
1101 final String chain, final String pdbfile)
1103 final StructureSelectionManagerProvider me = this;
1104 java.awt.EventQueue.invokeLater(new Runnable()
1111 StructureSelectionManager.getStructureSelectionManager(me)
1112 .mouseOverStructure(new Integer(pdbResNum).intValue(),
1116 System.err.println("mouseOver for '" + pdbResNum
1117 + "' in chain '" + chain + "' in structure '" + pdbfile
1120 } catch (NumberFormatException e)
1122 System.err.println("Ignoring invalid residue number string '"
1134 * jalview.bin.JalviewLiteJsApi#scrollViewToIn(jalview.appletgui.AlignFrame,
1135 * java.lang.String, java.lang.String)
1137 public void scrollViewToIn(final AlignFrame alf, final String topRow,
1138 final String leftHandColumn)
1140 java.awt.EventQueue.invokeLater(new Runnable()
1147 alf.scrollTo(new Integer(topRow).intValue(), new Integer(
1148 leftHandColumn).intValue());
1150 } catch (Exception ex)
1152 System.err.println("Couldn't parse integer arguments (topRow='"
1153 + topRow + "' and leftHandColumn='" + leftHandColumn
1155 ex.printStackTrace();
1165 * jalview.javascript.JalviewLiteJsApi#scrollViewToRowIn(jalview.appletgui
1166 * .AlignFrame, java.lang.String)
1169 public void scrollViewToRowIn(final AlignFrame alf, final String topRow)
1172 java.awt.EventQueue.invokeLater(new Runnable()
1179 alf.scrollToRow(new Integer(topRow).intValue());
1181 } catch (Exception ex)
1183 System.err.println("Couldn't parse integer arguments (topRow='"
1185 ex.printStackTrace();
1196 * jalview.javascript.JalviewLiteJsApi#scrollViewToColumnIn(jalview.appletgui
1197 * .AlignFrame, java.lang.String)
1200 public void scrollViewToColumnIn(final AlignFrame alf,
1201 final String leftHandColumn)
1203 java.awt.EventQueue.invokeLater(new Runnable()
1211 alf.scrollToColumn(new Integer(leftHandColumn).intValue());
1213 } catch (Exception ex)
1216 .println("Couldn't parse integer arguments (leftHandColumn='"
1217 + leftHandColumn + "')");
1218 ex.printStackTrace();
1225 // //////////////////////////////////////////////
1226 // //////////////////////////////////////////////
1228 public static int lastFrameX = 200;
1230 public static int lastFrameY = 200;
1232 boolean fileFound = true;
1234 String file = "No file";
1236 Button launcher = new Button("Start Jalview");
1239 * The currentAlignFrame is static, it will change if and when the user
1240 * selects a new window. Note that it will *never* point back to the embedded
1241 * AlignFrame if the applet is started as embedded on the page and then
1242 * afterwards a new view is created.
1244 public AlignFrame currentAlignFrame = null;
1247 * This is the first frame to be displayed, and does not change. API calls
1248 * will default to this instance if currentAlignFrame is null.
1250 AlignFrame initialAlignFrame = null;
1252 boolean embedded = false;
1254 private boolean checkForJmol = true;
1256 private boolean checkedForJmol = false; // ensure we don't check for jmol
1258 // every time the app is re-inited
1260 public boolean jmolAvailable = false;
1262 private boolean alignPdbStructures = false;
1265 * use an external structure viewer exclusively (no jmols or MCViews will be
1266 * opened by JalviewLite itself)
1268 public boolean useXtrnalSviewer = false;
1270 public static boolean debug = false;
1272 static String builddate = null, version = null, installation = null;
1274 private static void initBuildDetails()
1276 if (builddate == null)
1278 builddate = "unknown";
1280 installation = "Webstart";
1281 java.net.URL url = JalviewLite.class
1282 .getResource("/.build_properties");
1287 BufferedReader reader = new BufferedReader(new InputStreamReader(
1290 while ((line = reader.readLine()) != null)
1292 if (line.indexOf("VERSION") > -1)
1294 version = line.substring(line.indexOf("=") + 1);
1296 if (line.indexOf("BUILD_DATE") > -1)
1298 builddate = line.substring(line.indexOf("=") + 1);
1300 if (line.indexOf("INSTALLATION") > -1)
1302 installation = line.substring(line.indexOf("=") + 1);
1305 } catch (Exception ex)
1307 ex.printStackTrace();
1313 public static String getBuildDate()
1319 public static String getInstallation()
1322 return installation;
1325 public static String getVersion()
1331 // public JSObject scriptObject = null;
1334 * init method for Jalview Applet
1338 // remove any handlers that might be hanging around from an earlier instance
1343 System.err.println("Applet context is '"
1344 + getAppletContext().getClass().toString() + "'");
1346 JSObject scriptObject = JSObject.getWindow(this);
1347 if (debug && scriptObject != null)
1349 System.err.println("Applet has Javascript callback support.");
1352 } catch (Exception ex)
1355 .println("Warning: No JalviewLite javascript callbacks available.");
1358 ex.printStackTrace();
1362 * turn on extra applet debugging
1364 String dbg = getParameter("debug");
1367 debug = dbg.toLowerCase().equals("true");
1372 System.err.println("JalviewLite Version " + getVersion());
1373 System.err.println("Build Date : " + getBuildDate());
1374 System.err.println("Installation : " + getInstallation());
1377 String externalsviewer = getParameter("externalstructureviewer");
1378 if (externalsviewer != null)
1380 useXtrnalSviewer = externalsviewer.trim().toLowerCase()
1384 * if true disable the check for jmol
1386 String chkforJmol = getParameter("nojmol");
1387 if (chkforJmol != null)
1389 checkForJmol = !chkforJmol.equals("true");
1392 * get the separator parameter if present
1394 String sep = getParameter("separator");
1397 if (sep.length() > 0)
1402 System.err.println("Separator set to '" + separator + "'");
1407 throw new Error(MessageManager.getString("error.invalid_separator_parameter"));
1413 String param = getParameter("RGB");
1419 r = Integer.parseInt(param.substring(0, 2), 16);
1420 g = Integer.parseInt(param.substring(2, 4), 16);
1421 b = Integer.parseInt(param.substring(4, 6), 16);
1422 } catch (Exception ex)
1429 param = getParameter("label");
1432 launcher.setLabel(param);
1435 setBackground(new Color(r, g, b));
1437 file = getParameter("file");
1441 // Maybe the sequences are added as parameters
1442 StringBuffer data = new StringBuffer("PASTE");
1444 while ((file = getParameter("sequence" + i)) != null)
1446 data.append(file.toString() + "\n");
1449 if (data.length() > 5)
1451 file = data.toString();
1455 final JalviewLite jvapplet = this;
1456 if (getParameter("embedded") != null
1457 && getParameter("embedded").equalsIgnoreCase("true"))
1459 // Launch as embedded applet in page
1461 LoadingThread loader = new LoadingThread(file, jvapplet);
1464 else if (file != null)
1466 if (getParameter("showbutton") == null
1467 || !getParameter("showbutton").equalsIgnoreCase("false"))
1469 // Add the JalviewLite 'Button' to the page
1471 launcher.addActionListener(new java.awt.event.ActionListener()
1473 public void actionPerformed(ActionEvent e)
1475 LoadingThread loader = new LoadingThread(file, jvapplet);
1482 // Open jalviewLite immediately.
1483 LoadingThread loader = new LoadingThread(file, jvapplet);
1489 // jalview initialisation with no alignment. loadAlignment() method can
1490 // still be called to open new alignments.
1497 private void initLiveConnect()
1499 // try really hard to get the liveConnect thing working
1500 boolean notFailed = false;
1502 while (!notFailed && tries < 10)
1506 System.err.println("LiveConnect request thread going to sleep.");
1510 Thread.sleep(700 * (1 + tries));
1511 } catch (InterruptedException q)
1517 System.err.println("LiveConnect request thread woken up.");
1521 JSObject scriptObject = JSObject.getWindow(this);
1522 if (scriptObject.eval("navigator") != null)
1526 } catch (JSException jsex)
1528 System.err.println("Attempt " + tries
1529 + " to access LiveConnect javascript failed.");
1534 private void callInitCallback()
1536 String initjscallback = getParameter("oninit");
1537 if (initjscallback == null)
1541 initjscallback = initjscallback.trim();
1542 if (initjscallback.length() > 0)
1544 JSObject scriptObject = null;
1547 scriptObject = JSObject.getWindow(this);
1548 } catch (Exception ex)
1552 // try really hard to let the browser plugin know we want liveconnect
1555 if (scriptObject != null)
1559 // do onInit with the JS executor thread
1560 new JSFunctionExec(this).executeJavascriptFunction(true,
1561 initjscallback, null, "Calling oninit callback '"
1562 + initjscallback + "'.");
1563 } catch (Exception e)
1565 System.err.println("Exception when executing _oninit callback '"
1566 + initjscallback + "'.");
1567 e.printStackTrace();
1572 System.err.println("Not executing _oninit callback '"
1573 + initjscallback + "' - no scripting allowed.");
1579 * Initialises and displays a new java.awt.Frame
1582 * java.awt.Frame to be displayed
1584 * title of new frame
1586 * width if new frame
1588 * height of new frame
1590 public static void addFrame(final Frame frame, String title, int width,
1593 frame.setLocation(lastFrameX, lastFrameY);
1596 frame.setSize(width, height);
1597 frame.setTitle(title);
1598 frame.addWindowListener(new WindowAdapter()
1600 public void windowClosing(WindowEvent e)
1602 if (frame instanceof AlignFrame)
1604 AlignViewport vp = ((AlignFrame) frame).viewport;
1605 ((AlignFrame) frame).closeMenuItem_actionPerformed();
1606 if (vp.applet.currentAlignFrame == frame)
1608 vp.applet.currentAlignFrame = null;
1616 if (frame instanceof EmbmenuFrame)
1618 ((EmbmenuFrame) frame).destroyMenus();
1620 frame.setMenuBar(null);
1624 public void windowActivated(WindowEvent e)
1626 if (frame instanceof AlignFrame)
1628 ((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame;
1631 System.err.println("Activated window " + frame);
1635 super.windowActivated(e);
1638 * Probably not necessary to do this - see TODO above. (non-Javadoc)
1641 * java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent
1644 * public void windowDeactivated(WindowEvent e) { if (currentAlignFrame ==
1645 * frame) { currentAlignFrame = null; if (debug) {
1646 * System.err.println("Deactivated window "+frame); } }
1647 * super.windowDeactivated(e); }
1650 frame.setVisible(true);
1654 * This paints the background surrounding the "Launch Jalview button" <br>
1656 * If file given in parameter not found, displays error message
1661 public void paint(Graphics g)
1665 g.setColor(new Color(200, 200, 200));
1666 g.setColor(Color.cyan);
1667 g.fillRect(0, 0, getSize().width, getSize().height);
1668 g.setColor(Color.red);
1670 MessageManager.getString("label.jalview_cannot_open_file"),
1672 g.drawString("\"" + file + "\"", 5, 30);
1676 g.setColor(Color.black);
1677 g.setFont(new Font("Arial", Font.BOLD, 24));
1678 g.drawString(MessageManager.getString("label.jalview_applet"), 50,
1679 getSize().height / 2 - 30);
1680 g.drawString(MessageManager.getString("label.loading_data") + "...",
1681 50, getSize().height / 2);
1686 * get all components associated with the applet of the given type
1691 public Vector getAppletWindow(Class class1)
1693 Vector wnds = new Vector();
1694 Component[] cmp = getComponents();
1697 for (int i = 0; i < cmp.length; i++)
1699 if (class1.isAssignableFrom(cmp[i].getClass()))
1701 wnds.addElement(cmp);
1708 class LoadJmolThread extends Thread
1710 private boolean running = false;
1714 if (running || checkedForJmol)
1723 if (!System.getProperty("java.version").startsWith("1.1"))
1725 Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
1726 jmolAvailable = true;
1731 .println("Jmol not available - Using MCview for structures");
1733 } catch (java.lang.ClassNotFoundException ex)
1739 jmolAvailable = false;
1743 .println("Skipping Jmol check. Will use MCView (probably)");
1746 checkedForJmol = true;
1750 public boolean notFinished()
1752 return running || !checkedForJmol;
1756 class LoadingThread extends Thread
1759 * State variable: File source
1764 * State variable: protocol for access to file source
1769 * State variable: format of file source
1777 private void dbgMsg(String msg)
1781 System.err.println(msg);
1786 * update the protocol state variable for accessing the datasource located
1790 * @return possibly updated datasource string
1792 public String setProtocolState(String file)
1794 if (file.startsWith("PASTE"))
1796 file = file.substring(5);
1797 protocol = AppletFormatAdapter.PASTE;
1799 else if (inArchive(file))
1801 protocol = AppletFormatAdapter.CLASSLOADER;
1805 file = addProtocol(file);
1806 protocol = AppletFormatAdapter.URL;
1808 dbgMsg("Protocol identified as '" + protocol + "'");
1812 public LoadingThread(String _file, JalviewLite _applet)
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)
1834 // applet.callInitCallback();
1837 private void startLoading()
1839 AlignFrame newAlignFrame;
1840 dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");
1841 file = setProtocolState(_file);
1843 format = new jalview.io.IdentifyFile().Identify(file, protocol);
1844 dbgMsg("File identified as '" + format + "'");
1845 dbgMsg("Loading started.");
1846 Alignment al = null;
1849 al = new AppletFormatAdapter().readFile(file, protocol, format);
1850 } catch (java.io.IOException ex)
1852 dbgMsg("File load exception.");
1853 ex.printStackTrace();
1858 FileParse fp = new FileParse(file, protocol);
1860 dbgMsg(">>>Dumping contents of '" + file + "' " + "("
1862 while ((ln = fp.nextLine()) != null)
1866 dbgMsg(">>>Dump finished.");
1867 } catch (Exception e)
1870 .println("Exception when trying to dump the content of the file parameter.");
1871 e.printStackTrace();
1875 if ((al != null) && (al.getHeight() > 0))
1877 dbgMsg("Successfully loaded file.");
1878 newAlignFrame = new AlignFrame(al, applet, file, embedded);
1879 if (initialAlignFrame == null)
1881 initialAlignFrame = newAlignFrame;
1883 // update the focus.
1884 currentAlignFrame = newAlignFrame;
1886 if (protocol == jalview.io.AppletFormatAdapter.PASTE)
1888 newAlignFrame.setTitle(MessageManager.formatMessage(
1889 "label.sequences_from", new String[]
1890 { applet.getDocumentBase().toString() }));
1893 newAlignFrame.statusBar.setText(MessageManager.formatMessage(
1894 "label.successfully_loaded_file", new String[]
1897 String treeFile = applet.getParameter("tree");
1898 if (treeFile == null)
1900 treeFile = applet.getParameter("treeFile");
1903 if (treeFile != null)
1907 treeFile = setProtocolState(treeFile);
1909 * if (inArchive(treeFile)) { protocol =
1910 * AppletFormatAdapter.CLASSLOADER; } else { protocol =
1911 * AppletFormatAdapter.URL; treeFile = addProtocol(treeFile); }
1913 jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile,
1918 if (fin.getTree() != null)
1920 newAlignFrame.loadTree(fin, treeFile);
1921 dbgMsg("Successfuly imported tree.");
1925 dbgMsg("Tree parameter did not resolve to a valid tree.");
1927 } catch (Exception ex)
1929 ex.printStackTrace();
1934 * Try to load T-Coffee score file
1936 String sScoreFile = applet.getParameter("scoreFile");
1937 if (sScoreFile != null && !"".equals(sScoreFile))
1944 .println("Attempting to load T-COFFEE score file from the scoreFile parameter");
1946 if (!newAlignFrame.loadScoreFile(sScoreFile))
1949 .println("Failed to parse T-COFFEE parameter as a valid score file ('"
1950 + sScoreFile + "')");
1952 } catch (Exception e)
1954 System.err.printf("Cannot read score file: '%s'. Cause: %s \n",
1955 sScoreFile, e.getMessage());
1959 // ///////////////////////////
1960 // modify display of features
1961 // we do this before any features have been loaded, ensuring any hidden
1962 // groups are hidden when features first displayed
1964 // hide specific groups
1966 String param = applet.getParameter("hidefeaturegroups");
1969 newAlignFrame.setFeatureGroupState(separatorListToArray(param),
1971 // applet.setFeatureGroupStateOn(newAlignFrame, param, false);
1973 // show specific groups
1974 param = applet.getParameter("showfeaturegroups");
1977 newAlignFrame.setFeatureGroupState(separatorListToArray(param),
1979 // applet.setFeatureGroupStateOn(newAlignFrame, param, true);
1981 // and now load features
1982 param = applet.getParameter("features");
1985 param = setProtocolState(param);
1987 newAlignFrame.parseFeaturesFile(param, protocol);
1990 param = applet.getParameter("showFeatureSettings");
1991 if (param != null && param.equalsIgnoreCase("true"))
1993 newAlignFrame.viewport.showSequenceFeatures(true);
1994 new FeatureSettings(newAlignFrame.alignPanel);
1997 param = applet.getParameter("annotations");
2000 param = setProtocolState(param);
2002 if (new AnnotationFile().readAnnotationFile(
2003 newAlignFrame.viewport.getAlignment(), param, protocol))
2005 newAlignFrame.alignPanel.fontChanged();
2006 newAlignFrame.alignPanel.setScrollValues(0, 0);
2011 .println("Annotations were not added from annotation file '"
2017 param = applet.getParameter("jnetfile");
2022 param = setProtocolState(param);
2023 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
2025 JnetAnnotationMaker.add_annotation(predictions,
2026 newAlignFrame.viewport.getAlignment(), 0, false); // false==do
2034 newAlignFrame.alignPanel.fontChanged();
2035 newAlignFrame.alignPanel.setScrollValues(0, 0);
2036 } catch (Exception ex)
2038 ex.printStackTrace();
2042 * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6
2043 * - related to JAL-434
2045 applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",
2048 * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
2051 * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
2053 * <param name="PDBfile3" value="1q0o Q45135_9MICO">
2056 int pdbFileCount = 0;
2057 // Accumulate pdbs here if they are heading for the same view (if
2058 // alignPdbStructures is true)
2059 Vector pdbs = new Vector();
2060 // create a lazy matcher if we're asked to
2061 jalview.analysis.SequenceIdMatcher matcher = (applet
2062 .getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher(
2063 newAlignFrame.getAlignViewport().getAlignment()
2064 .getSequencesArray()) : null;
2068 if (pdbFileCount > 0)
2070 param = applet.getParameter("PDBFILE" + pdbFileCount);
2074 param = applet.getParameter("PDBFILE");
2079 PDBEntry pdb = new PDBEntry();
2082 SequenceI[] seqs = null;
2083 String[] chains = null;
2085 StringTokenizer st = new StringTokenizer(param, " ");
2087 if (st.countTokens() < 2)
2089 String sequence = applet.getParameter("PDBSEQ");
2090 if (sequence != null)
2092 seqs = new SequenceI[]
2093 { matcher == null ? (Sequence) newAlignFrame
2094 .getAlignViewport().getAlignment()
2095 .findName(sequence) : matcher.findIdMatch(sequence) };
2101 param = st.nextToken();
2102 Vector tmp = new Vector();
2103 Vector tmp2 = new Vector();
2105 while (st.hasMoreTokens())
2107 seqstring = st.nextToken();
2108 StringTokenizer st2 = new StringTokenizer(seqstring, "=");
2109 if (st2.countTokens() > 1)
2111 // This is the chain
2112 tmp2.addElement(st2.nextToken());
2113 seqstring = st2.nextToken();
2115 tmp.addElement(matcher == null ? (Sequence) newAlignFrame
2116 .getAlignViewport().getAlignment()
2117 .findName(seqstring) : matcher
2118 .findIdMatch(seqstring));
2121 seqs = new SequenceI[tmp.size()];
2123 if (tmp2.size() == tmp.size())
2125 chains = new String[tmp2.size()];
2126 tmp2.copyInto(chains);
2129 param = setProtocolState(param);
2131 if (// !jmolAvailable
2133 protocol == AppletFormatAdapter.CLASSLOADER
2134 && !useXtrnalSviewer)
2136 // Re: JAL-357 : the bug isn't a problem if we are using an
2138 // TODO: verify this Re:
2139 // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
2140 // This exception preserves the current behaviour where, even if
2141 // the local pdb file was identified in the class loader
2142 protocol = AppletFormatAdapter.URL; // this is probably NOT
2144 param = addProtocol(param); //
2151 for (int i = 0; i < seqs.length; i++)
2153 if (seqs[i] != null)
2155 ((Sequence) seqs[i]).addPDBId(pdb);
2156 StructureSelectionManager.getStructureSelectionManager(
2157 applet).registerPDBEntry(pdb);
2161 if (JalviewLite.debug)
2163 // this may not really be a problem but we give a warning
2166 .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
2172 if (!alignPdbStructures)
2174 newAlignFrame.newStructureView(applet, pdb, seqs, chains,
2179 pdbs.addElement(new Object[]
2180 { pdb, seqs, chains, new String(protocol) });
2186 } while (param != null || pdbFileCount < 10);
2187 if (pdbs.size() > 0)
2189 SequenceI[][] seqs = new SequenceI[pdbs.size()][];
2190 PDBEntry[] pdb = new PDBEntry[pdbs.size()];
2191 String[][] chains = new String[pdbs.size()][];
2192 String[] protocols = new String[pdbs.size()];
2193 for (int pdbsi = 0, pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)
2195 Object[] o = (Object[]) pdbs.elementAt(pdbsi);
2196 pdb[pdbsi] = (PDBEntry) o[0];
2197 seqs[pdbsi] = (SequenceI[]) o[1];
2198 chains[pdbsi] = (String[]) o[2];
2199 protocols[pdbsi] = (String) o[3];
2201 newAlignFrame.alignedStructureView(applet, pdb, seqs, chains,
2209 applet.remove(launcher);
2216 * Discovers whether the given file is in the Applet Archive
2222 boolean inArchive(String file)
2224 // This might throw a security exception in certain browsers
2225 // Netscape Communicator for instance.
2228 boolean rtn = (getClass().getResourceAsStream("/" + file) != null);
2231 System.err.println("Resource '" + file + "' was "
2232 + (rtn ? "" : "not") + " located by classloader.");
2235 } catch (Exception ex)
2237 System.out.println("Exception checking resources: " + file + " "
2243 String addProtocol(String file)
2245 if (file.indexOf("://") == -1)
2247 String fl = applet.resolveUrlForLocalOrAbsolute(file,
2251 if (new java.net.URL(fl).openStream() != null)
2255 System.err.println("Prepended document base for resource: '"
2260 } catch (Exception x)
2264 fl = applet.resolveUrlForLocalOrAbsolute(file, getCodeBase());
2267 if (new java.net.URL(fl).openStream() != null)
2271 System.err.println("Prepended codebase for resource: '"
2276 } catch (Exception x)
2288 * @return the default alignFrame acted on by the public applet methods. May
2289 * return null with an error message on System.err indicating the
2292 public AlignFrame getDefaultTargetFrame()
2294 if (currentAlignFrame != null)
2296 return currentAlignFrame;
2298 if (initialAlignFrame != null)
2300 return initialAlignFrame;
2303 .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
2308 * separator used for separatorList
2310 protected String separator = "" + ((char) 0x00AC); // the default used to be
2311 // '|' but many sequence
2312 // IDS include pipes.
2315 * set to enable the URL based javascript execution mechanism
2317 public boolean jsfallbackEnabled = false;
2320 * parse the string into a list
2323 * @return elements separated by separator
2325 public String[] separatorListToArray(String list)
2327 return separatorListToArray(list, separator);
2331 * parse the string into a list
2335 * @return elements separated by separator
2337 public String[] separatorListToArray(String list, String separator)
2339 // note separator local variable intentionally masks object field
2340 int seplen = separator.length();
2341 if (list == null || list.equals("") || list.equals(separator))
2345 java.util.Vector jv = new Vector();
2347 while ((pos = list.indexOf(separator, cp)) > cp)
2349 jv.addElement(list.substring(cp, pos));
2352 if (cp < list.length())
2354 String c = list.substring(cp);
2355 if (!c.equals(separator))
2362 String[] v = new String[jv.size()];
2363 for (int i = 0; i < v.length; i++)
2365 v[i] = (String) jv.elementAt(i);
2367 jv.removeAllElements();
2370 System.err.println("Array from '" + separator
2371 + "' separated List:\n" + v.length);
2372 for (int i = 0; i < v.length; i++)
2374 System.err.println("item " + i + " '" + v[i] + "'");
2381 System.err.println("Empty Array from '" + separator
2382 + "' separated List");
2388 * concatenate the list with separator
2391 * @return concatenated string
2393 public String arrayToSeparatorList(String[] list)
2395 return arrayToSeparatorList(list, separator);
2399 * concatenate the list with separator
2403 * @return concatenated string
2405 public String arrayToSeparatorList(String[] list, String separator)
2407 StringBuffer v = new StringBuffer();
2408 if (list != null && list.length > 0)
2410 for (int i = 0, iSize = list.length; i < iSize; i++)
2412 if (list[i] != null)
2416 v.append(separator);
2423 System.err.println("Returning '" + separator
2424 + "' separated List:\n");
2425 System.err.println(v);
2427 return v.toString();
2431 System.err.println("Returning empty '" + separator
2432 + "' separated List\n");
2434 return "" + separator;
2440 * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
2442 public String getFeatureGroups()
2444 String lst = arrayToSeparatorList(getDefaultTargetFrame()
2445 .getFeatureGroups());
2453 * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame
2456 public String getFeatureGroupsOn(AlignFrame alf)
2458 String lst = arrayToSeparatorList(alf.getFeatureGroups());
2465 * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)
2467 public String getFeatureGroupsOfState(boolean visible)
2469 return arrayToSeparatorList(getDefaultTargetFrame()
2470 .getFeatureGroupsOfState(visible));
2477 * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui
2478 * .AlignFrame, boolean)
2480 public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
2482 return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
2488 * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui.
2489 * AlignFrame, java.lang.String, boolean)
2491 public void setFeatureGroupStateOn(final AlignFrame alf,
2492 final String groups, boolean state)
2494 final boolean st = state;// !(state==null || state.equals("") ||
2495 // state.toLowerCase().equals("false"));
2496 java.awt.EventQueue.invokeLater(new Runnable()
2501 alf.setFeatureGroupState(separatorListToArray(groups), st);
2509 * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupState(java.lang.String,
2512 public void setFeatureGroupState(String groups, boolean state)
2514 setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
2520 * @see jalview.bin.JalviewLiteJsApi#getSeparator()
2522 public String getSeparator()
2530 * @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String)
2532 public void setSeparator(String separator)
2534 if (separator == null || separator.length() < 1)
2537 separator = "" + ((char) 0x00AC);
2539 this.separator = separator;
2542 System.err.println("Default Separator now: '" + separator + "'");
2547 * get boolean value of applet parameter 'name' and return default if
2548 * parameter is not set
2553 * the value to return otherwise
2554 * @return true or false
2556 public boolean getDefaultParameter(String name, boolean def)
2559 if ((stn = getParameter(name)) == null)
2563 if (stn.toLowerCase().equals("true"))
2573 * @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame,
2574 * java.lang.String, java.lang.String, java.lang.String)
2576 public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
2577 String pdbEntryString, String pdbFile)
2579 return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);
2582 protected void setAlignPdbStructures(boolean alignPdbStructures)
2584 this.alignPdbStructures = alignPdbStructures;
2587 public boolean isAlignPdbStructures()
2589 return alignPdbStructures;
2594 // callInitCallback();
2597 private Hashtable<String, long[]> jshashes = new Hashtable<String, long[]>();
2599 private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<String, Hashtable<String, String[]>>();
2601 public void setJsMessageSet(String messageclass, String viewId,
2602 String[] colcommands)
2604 Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
2607 msgset = new Hashtable<String, String[]>();
2608 jsmessages.put(messageclass, msgset);
2610 msgset.put(viewId, colcommands);
2611 long[] l = new long[colcommands.length];
2612 for (int i = 0; i < colcommands.length; i++)
2614 l[i] = colcommands[i].hashCode();
2616 jshashes.put(messageclass + "|" + viewId, l);
2622 * @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String,
2625 public String getJsMessage(String messageclass, String viewId)
2627 Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
2630 String[] msgs = msgset.get(viewId);
2633 for (int i = 0; i < msgs.length; i++)
2635 if (msgs[i] != null)
2647 public boolean isJsMessageSetChanged(String string, String string2,
2648 String[] colcommands)
2650 long[] l = jshashes.get(string + "|" + string2);
2651 if (l == null && colcommands != null)
2655 for (int i = 0; i < colcommands.length; i++)
2657 if (l[i] != colcommands[i].hashCode())
2665 private Vector jsExecQueue = new Vector();
2667 public Vector getJsExecQueue()
2672 public void setExecutor(JSFunctionExec jsFunctionExec2)
2674 jsFunctionExec = jsFunctionExec2;
2678 * return the given colour value parameter or the given default if parameter
2685 public Color getDefaultColourParameter(String colparam, Color defcolour)
2687 String colprop = getParameter(colparam);
2688 if (colprop == null || colprop.trim().length() == 0)
2692 Color col = jalview.schemes.ColourSchemeProperty
2693 .getAWTColorFromName(colprop);
2698 col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
2699 } catch (Exception ex)
2701 System.err.println("Couldn't parse '" + colprop
2702 + "' as a colour for " + colparam);
2706 return (col == null) ? defcolour : col;
2710 public void openJalviewHelpUrl()
2712 String helpUrl = getParameter("jalviewhelpurl");
2713 if (helpUrl == null || helpUrl.trim().length() < 5)
2715 helpUrl = "http://www.jalview.org/help.html";
2717 showURL(helpUrl, "HELP");
2721 * form a complete URL given a path to a resource and a reference location on
2725 * - an absolute path on the same server as localref or a document
2726 * located relative to localref
2728 * - a URL on the same server as url
2729 * @return a complete URL for the resource located by url
2731 private String resolveUrlForLocalOrAbsolute(String url, URL localref)
2733 String codebase = localref.toString();
2734 if (url.indexOf("/") == 0)
2736 url = codebase.substring(0, codebase.length()
2737 - localref.getFile().length())
2742 url = localref + url;
2748 * open a URL in the browser - resolving it according to relative refs and
2749 * coping with javascript: protocol if necessary.
2754 public void showURL(String url, String target)
2758 if (url.indexOf(":") == -1)
2760 // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
2762 // Should really use docbase, not codebase.
2764 url = resolveUrlForLocalOrAbsolute(
2766 prepend = getDefaultParameter("resolvetocodebase", false) ? getDocumentBase()
2771 .println("Show url (prepended "
2773 + " - toggle resolvetocodebase if code/docbase resolution is wrong): "
2781 System.err.println("Show url: " + url);
2784 if (url.indexOf("javascript:") == 0)
2786 // no target for the javascript context
2787 getAppletContext().showDocument(new java.net.URL(url));
2791 getAppletContext().showDocument(new java.net.URL(url), target);
2793 } catch (Exception ex)
2795 ex.printStackTrace();
2800 * bind structures in a viewer to any matching sequences in an alignFrame (use
2801 * sequenceIds to limit scope of search to specific sequences)
2805 * @param sequenceIds
2806 * @return TODO: consider making an exception structure for indicating when
2807 * binding fails public SequenceStructureBinding
2808 * addStructureViewInstance( AlignFrame alFrame, Object viewer, String
2811 * if (sequenceIds != null && sequenceIds.length() > 0) { return
2812 * alFrame.addStructureViewInstance(viewer,
2813 * separatorListToArray(sequenceIds)); } else { return
2814 * alFrame.addStructureViewInstance(viewer, null); } // return null; }