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.StringTokenizer;
64 import java.util.Vector;
66 import netscape.javascript.JSException;
67 import netscape.javascript.JSObject;
70 * Jalview Applet. Runs in Java 1.18 runtime
73 * @version $Revision: 1.92 $
75 public class JalviewLite extends Applet implements
76 StructureSelectionManagerProvider, JalviewLiteJsApi
79 public StructureSelectionManager getStructureSelectionManager()
81 return StructureSelectionManager.getStructureSelectionManager(this);
84 // /////////////////////////////////////////
85 // The following public methods maybe called
86 // externally, eg via javascript in HTML page
90 * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences()
92 public String getSelectedSequences()
94 return getSelectedSequencesFrom(getDefaultTargetFrame());
100 * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
102 public String getSelectedSequences(String sep)
104 return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);
111 * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
114 public String getSelectedSequencesFrom(AlignFrame alf)
116 return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);
123 * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
124 * .AlignFrame, java.lang.String)
126 public String getSelectedSequencesFrom(AlignFrame alf, String sep)
128 StringBuffer result = new StringBuffer("");
129 if (sep == null || sep.length() == 0)
131 sep = separator; // "+0x00AC;
133 if (alf.viewport.getSelectionGroup() != null)
135 SequenceI[] seqs = alf.viewport.getSelectionGroup()
136 .getSequencesInOrder(alf.viewport.getAlignment());
138 for (int i = 0; i < seqs.length; i++)
140 result.append(seqs[i].getName());
145 return result.toString();
151 * @see jalview.bin.JalviewLiteJsApi#highlight(java.lang.String,
152 * java.lang.String, java.lang.String)
154 public void highlight(String sequenceId, String position,
155 String alignedPosition)
157 highlightIn(getDefaultTargetFrame(), sequenceId, position,
164 * @see jalview.bin.JalviewLiteJsApi#highlightIn(jalview.appletgui.AlignFrame,
165 * java.lang.String, java.lang.String, java.lang.String)
167 public void highlightIn(final AlignFrame alf, final String sequenceId,
168 final String position, final String alignedPosition)
170 // TODO: could try to highlight in all alignments if alf==null
171 jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
172 alf.viewport.getAlignment().getSequencesArray());
173 final SequenceI sq = matcher.findIdMatch(sequenceId);
179 apos = new Integer(position).intValue();
181 } catch (NumberFormatException ex)
185 final StructureSelectionManagerProvider me = this;
186 final int pos = apos;
187 // use vamsas listener to broadcast to all listeners in scope
188 if (alignedPosition != null
189 && (alignedPosition.trim().length() == 0 || alignedPosition
190 .toLowerCase().indexOf("false") > -1))
192 java.awt.EventQueue.invokeLater(new Runnable()
197 StructureSelectionManager.getStructureSelectionManager(me)
198 .mouseOverVamsasSequence(sq, sq.findIndex(pos), null);
204 java.awt.EventQueue.invokeLater(new Runnable()
209 StructureSelectionManager.getStructureSelectionManager(me)
210 .mouseOverVamsasSequence(sq, pos, null);
220 * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
223 public void select(String sequenceIds, String columns)
225 selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator);
231 * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
232 * java.lang.String, java.lang.String)
234 public void select(String sequenceIds, String columns, String sep)
236 selectIn(getDefaultTargetFrame(), sequenceIds, columns, sep);
242 * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
243 * java.lang.String, java.lang.String)
245 public void selectIn(AlignFrame alf, String sequenceIds, String columns)
247 selectIn(alf, sequenceIds, columns, separator);
253 * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
254 * java.lang.String, java.lang.String, java.lang.String)
256 public void selectIn(final AlignFrame alf, String sequenceIds,
257 String columns, String sep)
259 if (sep == null || sep.length() == 0)
267 System.err.println("Selecting region using separator string '"
272 String[] ids = separatorListToArray(sequenceIds, sep);
273 String[] cols = separatorListToArray(columns, sep);
274 final SequenceGroup sel = new SequenceGroup();
275 final ColumnSelection csel = new ColumnSelection();
276 AlignmentI al = alf.viewport.getAlignment();
277 jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
278 alf.viewport.getAlignment().getSequencesArray());
279 int start = 0, end = al.getWidth(), alw = al.getWidth();
280 boolean seqsfound = true;
281 if (ids != null && ids.length > 0)
284 for (int i = 0; i < ids.length; i++)
286 if (ids[i].trim().length() == 0)
290 SequenceI sq = matcher.findIdMatch(ids[i]);
294 sel.addSequence(sq, false);
298 boolean inseqpos = false;
299 if (cols != null && cols.length > 0)
301 boolean seset = false;
302 for (int i = 0; i < cols.length; i++)
304 String cl = cols[i].trim();
305 if (cl.length() == 0)
310 if ((p = cl.indexOf("-")) > -1)
312 int from = -1, to = -1;
315 from = new Integer(cl.substring(0, p)).intValue();
317 } catch (NumberFormatException ex)
320 .println("ERROR: Couldn't parse first integer in range element column selection string '"
321 + cl + "' - format is 'from-to'");
326 to = new Integer(cl.substring(p + 1)).intValue();
328 } catch (NumberFormatException ex)
331 .println("ERROR: Couldn't parse second integer in range element column selection string '"
332 + cl + "' - format is 'from-to'");
335 if (from >= 0 && to >= 0)
352 // comment to prevent range extension
362 for (int r = from; r <= to; r++)
364 if (r >= 0 && r < alw)
371 System.err.println("Range '" + cl + "' deparsed as [" + from
377 System.err.println("ERROR: Invalid Range '" + cl
378 + "' deparsed as [" + from + "," + to + "]");
386 r = new Integer(cl).intValue();
388 } catch (NumberFormatException ex)
390 if (cl.toLowerCase().equals("sequence"))
392 // we are in the dataset sequence's coordinate frame.
398 .println("ERROR: Couldn't parse integer from point selection element of column selection string '"
403 if (r >= 0 && r <= alw)
413 // comment to prevent range extension
426 System.err.println("Point selection '" + cl
427 + "' deparsed as [" + r + "]");
432 System.err.println("ERROR: Invalid Point selection '" + cl
433 + "' deparsed as [" + r + "]");
440 // we only propagate the selection when it was the null selection, or the
441 // given sequences were found in the alignment.
442 if (inseqpos && sel.getSize() > 0)
444 // assume first sequence provides reference frame ?
445 SequenceI rs = sel.getSequenceAt(0);
446 start = rs.findIndex(start);
447 end = rs.findIndex(end);
450 Vector cs = csel.getSelected();
452 for (int csi = 0, csiS = cs.size(); csi < csiS; csi++)
454 csel.addElement(rs.findIndex(((Integer) cs.elementAt(csi))
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;
1274 private static void initBuildDetails()
1276 if (builddate == null)
1278 builddate = "unknown";
1280 java.net.URL url = JalviewLite.class
1281 .getResource("/.build_properties");
1286 BufferedReader reader = new BufferedReader(new InputStreamReader(
1289 while ((line = reader.readLine()) != null)
1291 if (line.indexOf("VERSION") > -1)
1293 version = line.substring(line.indexOf("=") + 1);
1295 if (line.indexOf("BUILD_DATE") > -1)
1297 builddate = line.substring(line.indexOf("=") + 1);
1300 } catch (Exception ex)
1302 ex.printStackTrace();
1308 public static String getBuildDate()
1314 public static String getVersion()
1320 // public JSObject scriptObject = null;
1323 * init method for Jalview Applet
1327 // remove any handlers that might be hanging around from an earlier instance
1332 System.err.println("Applet context is '"
1333 + getAppletContext().getClass().toString() + "'");
1335 JSObject scriptObject = JSObject.getWindow(this);
1336 if (debug && scriptObject != null)
1338 System.err.println("Applet has Javascript callback support.");
1341 } catch (Exception ex)
1344 .println("Warning: No JalviewLite javascript callbacks available.");
1347 ex.printStackTrace();
1351 * turn on extra applet debugging
1353 String dbg = getParameter("debug");
1356 debug = dbg.toLowerCase().equals("true");
1361 System.err.println("JalviewLite Version " + getVersion());
1362 System.err.println("Build Date : " + getBuildDate());
1365 String externalsviewer = getParameter("externalstructureviewer");
1366 if (externalsviewer != null)
1368 useXtrnalSviewer = externalsviewer.trim().toLowerCase()
1372 * if true disable the check for jmol
1374 String chkforJmol = getParameter("nojmol");
1375 if (chkforJmol != null)
1377 checkForJmol = !chkforJmol.equals("true");
1380 * get the separator parameter if present
1382 String sep = getParameter("separator");
1385 if (sep.length() > 0)
1390 System.err.println("Separator set to '" + separator + "'");
1396 "Invalid separator parameter - must be non-zero length");
1402 String param = getParameter("RGB");
1408 r = Integer.parseInt(param.substring(0, 2), 16);
1409 g = Integer.parseInt(param.substring(2, 4), 16);
1410 b = Integer.parseInt(param.substring(4, 6), 16);
1411 } catch (Exception ex)
1418 param = getParameter("label");
1421 launcher.setLabel(param);
1424 setBackground(new Color(r, g, b));
1426 file = getParameter("file");
1430 // Maybe the sequences are added as parameters
1431 StringBuffer data = new StringBuffer("PASTE");
1433 while ((file = getParameter("sequence" + i)) != null)
1435 data.append(file.toString() + "\n");
1438 if (data.length() > 5)
1440 file = data.toString();
1444 final JalviewLite jvapplet = this;
1445 if (getParameter("embedded") != null
1446 && getParameter("embedded").equalsIgnoreCase("true"))
1448 // Launch as embedded applet in page
1450 LoadingThread loader = new LoadingThread(file, jvapplet);
1453 else if (file != null)
1455 if (getParameter("showbutton") == null
1456 || !getParameter("showbutton").equalsIgnoreCase("false"))
1458 // Add the JalviewLite 'Button' to the page
1460 launcher.addActionListener(new java.awt.event.ActionListener()
1462 public void actionPerformed(ActionEvent e)
1464 LoadingThread loader = new LoadingThread(file, jvapplet);
1471 // Open jalviewLite immediately.
1472 LoadingThread loader = new LoadingThread(file, jvapplet);
1478 // jalview initialisation with no alignment. loadAlignment() method can
1479 // still be called to open new alignments.
1486 private void initLiveConnect()
1488 // try really hard to get the liveConnect thing working
1489 boolean notFailed = false;
1491 while (!notFailed && tries < 10)
1495 System.err.println("LiveConnect request thread going to sleep.");
1499 Thread.sleep(700 * (1 + tries));
1500 } catch (InterruptedException q)
1506 System.err.println("LiveConnect request thread woken up.");
1510 JSObject scriptObject = JSObject.getWindow(this);
1511 if (scriptObject.eval("navigator") != null)
1515 } catch (JSException jsex)
1517 System.err.println("Attempt " + tries
1518 + " to access LiveConnect javascript failed.");
1523 private void callInitCallback()
1525 String initjscallback = getParameter("oninit");
1526 if (initjscallback == null)
1530 initjscallback = initjscallback.trim();
1531 if (initjscallback.length() > 0)
1533 JSObject scriptObject = null;
1536 scriptObject = JSObject.getWindow(this);
1537 } catch (Exception ex)
1541 // try really hard to let the browser plugin know we want liveconnect
1544 if (scriptObject != null)
1548 // do onInit with the JS executor thread
1549 new JSFunctionExec(this).executeJavascriptFunction(true,
1550 initjscallback, null, "Calling oninit callback '"
1551 + initjscallback + "'.");
1552 } catch (Exception e)
1554 System.err.println("Exception when executing _oninit callback '"
1555 + initjscallback + "'.");
1556 e.printStackTrace();
1561 System.err.println("Not executing _oninit callback '"
1562 + initjscallback + "' - no scripting allowed.");
1568 * Initialises and displays a new java.awt.Frame
1571 * java.awt.Frame to be displayed
1573 * title of new frame
1575 * width if new frame
1577 * height of new frame
1579 public static void addFrame(final Frame frame, String title, int width,
1582 frame.setLocation(lastFrameX, lastFrameY);
1585 frame.setSize(width, height);
1586 frame.setTitle(title);
1587 frame.addWindowListener(new WindowAdapter()
1589 public void windowClosing(WindowEvent e)
1591 if (frame instanceof AlignFrame)
1593 AlignViewport vp = ((AlignFrame) frame).viewport;
1594 ((AlignFrame) frame).closeMenuItem_actionPerformed();
1595 if (vp.applet.currentAlignFrame == frame)
1597 vp.applet.currentAlignFrame = null;
1605 if (frame instanceof EmbmenuFrame)
1607 ((EmbmenuFrame) frame).destroyMenus();
1609 frame.setMenuBar(null);
1613 public void windowActivated(WindowEvent e)
1615 if (frame instanceof AlignFrame)
1617 ((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame;
1620 System.err.println("Activated window " + frame);
1624 super.windowActivated(e);
1627 * Probably not necessary to do this - see TODO above. (non-Javadoc)
1630 * java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent
1633 * public void windowDeactivated(WindowEvent e) { if (currentAlignFrame ==
1634 * frame) { currentAlignFrame = null; if (debug) {
1635 * System.err.println("Deactivated window "+frame); } }
1636 * super.windowDeactivated(e); }
1639 frame.setVisible(true);
1643 * This paints the background surrounding the "Launch Jalview button" <br>
1645 * If file given in parameter not found, displays error message
1650 public void paint(Graphics g)
1654 g.setColor(new Color(200, 200, 200));
1655 g.setColor(Color.cyan);
1656 g.fillRect(0, 0, getSize().width, getSize().height);
1657 g.setColor(Color.red);
1659 MessageManager.getString("label.jalview_cannot_open_file"),
1661 g.drawString("\"" + file + "\"", 5, 30);
1665 g.setColor(Color.black);
1666 g.setFont(new Font("Arial", Font.BOLD, 24));
1667 g.drawString(MessageManager.getString("label.jalview_applet"), 50,
1668 getSize().height / 2 - 30);
1669 g.drawString(MessageManager.getString("label.loading_data") + "...",
1670 50, getSize().height / 2);
1675 * get all components associated with the applet of the given type
1680 public Vector getAppletWindow(Class class1)
1682 Vector wnds = new Vector();
1683 Component[] cmp = getComponents();
1686 for (int i = 0; i < cmp.length; i++)
1688 if (class1.isAssignableFrom(cmp[i].getClass()))
1690 wnds.addElement(cmp);
1697 class LoadJmolThread extends Thread
1699 private boolean running = false;
1703 if (running || checkedForJmol)
1712 if (!System.getProperty("java.version").startsWith("1.1"))
1714 Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
1715 jmolAvailable = true;
1720 .println("Jmol not available - Using MCview for structures");
1722 } catch (java.lang.ClassNotFoundException ex)
1728 jmolAvailable = false;
1732 .println("Skipping Jmol check. Will use MCView (probably)");
1735 checkedForJmol = true;
1739 public boolean notFinished()
1741 return running || !checkedForJmol;
1745 class LoadingThread extends Thread
1748 * State variable: File source
1753 * State variable: protocol for access to file source
1758 * State variable: format of file source
1766 private void dbgMsg(String msg)
1770 System.err.println(msg);
1775 * update the protocol state variable for accessing the datasource located
1779 * @return possibly updated datasource string
1781 public String setProtocolState(String file)
1783 if (file.startsWith("PASTE"))
1785 file = file.substring(5);
1786 protocol = AppletFormatAdapter.PASTE;
1788 else if (inArchive(file))
1790 protocol = AppletFormatAdapter.CLASSLOADER;
1794 file = addProtocol(file);
1795 protocol = AppletFormatAdapter.URL;
1797 dbgMsg("Protocol identified as '" + protocol + "'");
1801 public LoadingThread(String _file, JalviewLite _applet)
1809 LoadJmolThread jmolchecker = new LoadJmolThread();
1810 jmolchecker.start();
1811 while (jmolchecker.notFinished())
1813 // wait around until the Jmol check is complete.
1817 } catch (Exception e)
1823 // applet.callInitCallback();
1826 private void startLoading()
1828 AlignFrame newAlignFrame;
1829 dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");
1830 file = setProtocolState(_file);
1832 format = new jalview.io.IdentifyFile().Identify(file, protocol);
1833 dbgMsg("File identified as '" + format + "'");
1834 dbgMsg("Loading started.");
1835 Alignment al = null;
1838 al = new AppletFormatAdapter().readFile(file, protocol, format);
1839 } catch (java.io.IOException ex)
1841 dbgMsg("File load exception.");
1842 ex.printStackTrace();
1847 FileParse fp = new FileParse(file, protocol);
1849 dbgMsg(">>>Dumping contents of '" + file + "' " + "("
1851 while ((ln = fp.nextLine()) != null)
1855 dbgMsg(">>>Dump finished.");
1856 } catch (Exception e)
1859 .println("Exception when trying to dump the content of the file parameter.");
1860 e.printStackTrace();
1864 if ((al != null) && (al.getHeight() > 0))
1866 dbgMsg("Successfully loaded file.");
1867 newAlignFrame = new AlignFrame(al, applet, file, embedded);
1868 if (initialAlignFrame == null)
1870 initialAlignFrame = newAlignFrame;
1872 // update the focus.
1873 currentAlignFrame = newAlignFrame;
1875 if (protocol == jalview.io.AppletFormatAdapter.PASTE)
1877 newAlignFrame.setTitle(MessageManager.formatMessage(
1878 "label.sequences_from", new String[]
1879 { applet.getDocumentBase().toString() }));
1882 newAlignFrame.statusBar.setText(MessageManager.formatMessage(
1883 "label.successfully_loaded_file", new String[]
1886 String treeFile = applet.getParameter("tree");
1887 if (treeFile == null)
1889 treeFile = applet.getParameter("treeFile");
1892 if (treeFile != null)
1896 treeFile = setProtocolState(treeFile);
1898 * if (inArchive(treeFile)) { protocol =
1899 * AppletFormatAdapter.CLASSLOADER; } else { protocol =
1900 * AppletFormatAdapter.URL; treeFile = addProtocol(treeFile); }
1902 jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile,
1907 if (fin.getTree() != null)
1909 newAlignFrame.loadTree(fin, treeFile);
1910 dbgMsg("Successfuly imported tree.");
1914 dbgMsg("Tree parameter did not resolve to a valid tree.");
1916 } catch (Exception ex)
1918 ex.printStackTrace();
1923 * Try to load T-Coffee score file
1925 String sScoreFile = applet.getParameter("scoreFile");
1926 if (sScoreFile != null && !"".equals(sScoreFile))
1933 .println("Attempting to load T-COFFEE score file from the scoreFile parameter");
1935 if (!newAlignFrame.loadScoreFile(sScoreFile))
1938 .println("Failed to parse T-COFFEE parameter as a valid score file ('"
1939 + sScoreFile + "')");
1941 } catch (Exception e)
1943 System.err.printf("Cannot read score file: '%s'. Cause: %s \n",
1944 sScoreFile, e.getMessage());
1948 // ///////////////////////////
1949 // modify display of features
1950 // we do this before any features have been loaded, ensuring any hidden
1951 // groups are hidden when features first displayed
1953 // hide specific groups
1955 String param = applet.getParameter("hidefeaturegroups");
1958 newAlignFrame.setFeatureGroupState(separatorListToArray(param),
1960 // applet.setFeatureGroupStateOn(newAlignFrame, param, false);
1962 // show specific groups
1963 param = applet.getParameter("showfeaturegroups");
1966 newAlignFrame.setFeatureGroupState(separatorListToArray(param),
1968 // applet.setFeatureGroupStateOn(newAlignFrame, param, true);
1970 // and now load features
1971 param = applet.getParameter("features");
1974 param = setProtocolState(param);
1976 newAlignFrame.parseFeaturesFile(param, protocol);
1979 param = applet.getParameter("showFeatureSettings");
1980 if (param != null && param.equalsIgnoreCase("true"))
1982 newAlignFrame.viewport.showSequenceFeatures(true);
1983 new FeatureSettings(newAlignFrame.alignPanel);
1986 param = applet.getParameter("annotations");
1989 param = setProtocolState(param);
1991 if (new AnnotationFile().readAnnotationFile(
1992 newAlignFrame.viewport.getAlignment(), param, protocol))
1994 newAlignFrame.alignPanel.fontChanged();
1995 newAlignFrame.alignPanel.setScrollValues(0, 0);
2000 .println("Annotations were not added from annotation file '"
2006 param = applet.getParameter("jnetfile");
2011 param = setProtocolState(param);
2012 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
2014 JnetAnnotationMaker.add_annotation(predictions,
2015 newAlignFrame.viewport.getAlignment(), 0, false); // false==do
2023 newAlignFrame.alignPanel.fontChanged();
2024 newAlignFrame.alignPanel.setScrollValues(0, 0);
2025 } catch (Exception ex)
2027 ex.printStackTrace();
2031 * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6
2032 * - related to JAL-434
2034 applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",
2037 * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
2040 * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
2042 * <param name="PDBfile3" value="1q0o Q45135_9MICO">
2045 int pdbFileCount = 0;
2046 // Accumulate pdbs here if they are heading for the same view (if
2047 // alignPdbStructures is true)
2048 Vector pdbs = new Vector();
2049 // create a lazy matcher if we're asked to
2050 jalview.analysis.SequenceIdMatcher matcher = (applet
2051 .getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher(
2052 newAlignFrame.getAlignViewport().getAlignment()
2053 .getSequencesArray()) : null;
2057 if (pdbFileCount > 0)
2059 param = applet.getParameter("PDBFILE" + pdbFileCount);
2063 param = applet.getParameter("PDBFILE");
2068 PDBEntry pdb = new PDBEntry();
2071 SequenceI[] seqs = null;
2072 String[] chains = null;
2074 StringTokenizer st = new StringTokenizer(param, " ");
2076 if (st.countTokens() < 2)
2078 String sequence = applet.getParameter("PDBSEQ");
2079 if (sequence != null)
2080 seqs = new SequenceI[]
2081 { matcher == null ? (Sequence) newAlignFrame
2082 .getAlignViewport().getAlignment()
2083 .findName(sequence) : matcher.findIdMatch(sequence) };
2088 param = st.nextToken();
2089 Vector tmp = new Vector();
2090 Vector tmp2 = new Vector();
2092 while (st.hasMoreTokens())
2094 seqstring = st.nextToken();
2095 StringTokenizer st2 = new StringTokenizer(seqstring, "=");
2096 if (st2.countTokens() > 1)
2098 // This is the chain
2099 tmp2.addElement(st2.nextToken());
2100 seqstring = st2.nextToken();
2102 tmp.addElement(matcher == null ? (Sequence) newAlignFrame
2103 .getAlignViewport().getAlignment()
2104 .findName(seqstring) : matcher
2105 .findIdMatch(seqstring));
2108 seqs = new SequenceI[tmp.size()];
2110 if (tmp2.size() == tmp.size())
2112 chains = new String[tmp2.size()];
2113 tmp2.copyInto(chains);
2116 param = setProtocolState(param);
2118 if (// !jmolAvailable
2120 protocol == AppletFormatAdapter.CLASSLOADER
2121 && !useXtrnalSviewer)
2123 // Re: JAL-357 : the bug isn't a problem if we are using an
2125 // TODO: verify this Re:
2126 // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
2127 // This exception preserves the current behaviour where, even if
2128 // the local pdb file was identified in the class loader
2129 protocol = AppletFormatAdapter.URL; // this is probably NOT
2131 param = addProtocol(param); //
2138 for (int i = 0; i < seqs.length; i++)
2140 if (seqs[i] != null)
2142 ((Sequence) seqs[i]).addPDBId(pdb);
2146 if (JalviewLite.debug)
2148 // this may not really be a problem but we give a warning
2151 .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
2157 if (!alignPdbStructures)
2159 newAlignFrame.newStructureView(applet, pdb, seqs, chains,
2164 pdbs.addElement(new Object[]
2165 { pdb, seqs, chains, new String(protocol) });
2171 } while (param != null || pdbFileCount < 10);
2172 if (pdbs.size() > 0)
2174 SequenceI[][] seqs = new SequenceI[pdbs.size()][];
2175 PDBEntry[] pdb = new PDBEntry[pdbs.size()];
2176 String[][] chains = new String[pdbs.size()][];
2177 String[] protocols = new String[pdbs.size()];
2178 for (int pdbsi = 0, pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)
2180 Object[] o = (Object[]) pdbs.elementAt(pdbsi);
2181 pdb[pdbsi] = (PDBEntry) o[0];
2182 seqs[pdbsi] = (SequenceI[]) o[1];
2183 chains[pdbsi] = (String[]) o[2];
2184 protocols[pdbsi] = (String) o[3];
2186 newAlignFrame.alignedStructureView(applet, pdb, seqs, chains,
2194 applet.remove(launcher);
2201 * Discovers whether the given file is in the Applet Archive
2207 boolean inArchive(String file)
2209 // This might throw a security exception in certain browsers
2210 // Netscape Communicator for instance.
2213 boolean rtn = (getClass().getResourceAsStream("/" + file) != null);
2216 System.err.println("Resource '" + file + "' was "
2217 + (rtn ? "" : "not") + " located by classloader.");
2220 } catch (Exception ex)
2222 System.out.println("Exception checking resources: " + file + " "
2228 String addProtocol(String file)
2230 if (file.indexOf("://") == -1)
2232 String fl = applet.resolveUrlForLocalOrAbsolute(file,
2236 if (new java.net.URL(fl).openStream() != null)
2240 System.err.println("Prepended document base for resource: '"
2245 } catch (Exception x)
2249 fl = applet.resolveUrlForLocalOrAbsolute(file, getCodeBase());
2252 if (new java.net.URL(fl).openStream() != null)
2256 System.err.println("Prepended codebase for resource: '"
2261 } catch (Exception x)
2273 * @return the default alignFrame acted on by the public applet methods. May
2274 * return null with an error message on System.err indicating the
2277 public AlignFrame getDefaultTargetFrame()
2279 if (currentAlignFrame != null)
2281 return currentAlignFrame;
2283 if (initialAlignFrame != null)
2285 return initialAlignFrame;
2288 .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
2293 * separator used for separatorList
2295 protected String separator = "" + ((char) 0x00AC); // the default used to be
2296 // '|' but many sequence
2297 // IDS include pipes.
2300 * set to enable the URL based javascript execution mechanism
2302 public boolean jsfallbackEnabled = false;
2305 * parse the string into a list
2308 * @return elements separated by separator
2310 public String[] separatorListToArray(String list)
2312 return separatorListToArray(list, separator);
2316 * parse the string into a list
2320 * @return elements separated by separator
2322 public String[] separatorListToArray(String list, String separator)
2324 // note separator local variable intentionally masks object field
2325 int seplen = separator.length();
2326 if (list == null || list.equals("") || list.equals(separator))
2328 java.util.Vector jv = new Vector();
2330 while ((pos = list.indexOf(separator, cp)) > cp)
2332 jv.addElement(list.substring(cp, pos));
2335 if (cp < list.length())
2337 String c = list.substring(cp);
2338 if (!c.equals(separator))
2345 String[] v = new String[jv.size()];
2346 for (int i = 0; i < v.length; i++)
2348 v[i] = (String) jv.elementAt(i);
2350 jv.removeAllElements();
2353 System.err.println("Array from '" + separator
2354 + "' separated List:\n" + v.length);
2355 for (int i = 0; i < v.length; i++)
2357 System.err.println("item " + i + " '" + v[i] + "'");
2364 System.err.println("Empty Array from '" + separator
2365 + "' separated List");
2371 * concatenate the list with separator
2374 * @return concatenated string
2376 public String arrayToSeparatorList(String[] list)
2378 return arrayToSeparatorList(list, separator);
2382 * concatenate the list with separator
2386 * @return concatenated string
2388 public String arrayToSeparatorList(String[] list, String separator)
2390 StringBuffer v = new StringBuffer();
2391 if (list != null && list.length > 0)
2393 for (int i = 0, iSize = list.length; i < iSize; i++)
2395 if (list[i] != null)
2399 v.append(separator);
2406 System.err.println("Returning '" + separator
2407 + "' separated List:\n");
2408 System.err.println(v);
2410 return v.toString();
2414 System.err.println("Returning empty '" + separator
2415 + "' separated List\n");
2417 return "" + separator;
2423 * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
2425 public String getFeatureGroups()
2427 String lst = arrayToSeparatorList(getDefaultTargetFrame()
2428 .getFeatureGroups());
2436 * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame
2439 public String getFeatureGroupsOn(AlignFrame alf)
2441 String lst = arrayToSeparatorList(alf.getFeatureGroups());
2448 * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)
2450 public String getFeatureGroupsOfState(boolean visible)
2452 return arrayToSeparatorList(getDefaultTargetFrame()
2453 .getFeatureGroupsOfState(visible));
2460 * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui
2461 * .AlignFrame, boolean)
2463 public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
2465 return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
2471 * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui.
2472 * AlignFrame, java.lang.String, boolean)
2474 public void setFeatureGroupStateOn(final AlignFrame alf,
2475 final String groups, boolean state)
2477 final boolean st = state;// !(state==null || state.equals("") ||
2478 // state.toLowerCase().equals("false"));
2479 java.awt.EventQueue.invokeLater(new Runnable()
2484 alf.setFeatureGroupState(separatorListToArray(groups), st);
2492 * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupState(java.lang.String,
2495 public void setFeatureGroupState(String groups, boolean state)
2497 setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
2503 * @see jalview.bin.JalviewLiteJsApi#getSeparator()
2505 public String getSeparator()
2513 * @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String)
2515 public void setSeparator(String separator)
2517 if (separator == null || separator.length() < 1)
2520 separator = "" + ((char) 0x00AC);
2522 this.separator = separator;
2525 System.err.println("Default Separator now: '" + separator + "'");
2530 * get boolean value of applet parameter 'name' and return default if
2531 * parameter is not set
2536 * the value to return otherwise
2537 * @return true or false
2539 public boolean getDefaultParameter(String name, boolean def)
2542 if ((stn = getParameter(name)) == null)
2546 if (stn.toLowerCase().equals("true"))
2556 * @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame,
2557 * java.lang.String, java.lang.String, java.lang.String)
2559 public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
2560 String pdbEntryString, String pdbFile)
2562 return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);
2565 protected void setAlignPdbStructures(boolean alignPdbStructures)
2567 this.alignPdbStructures = alignPdbStructures;
2570 public boolean isAlignPdbStructures()
2572 return alignPdbStructures;
2577 // callInitCallback();
2580 private Hashtable<String, long[]> jshashes = new Hashtable<String, long[]>();
2582 private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<String, Hashtable<String, String[]>>();
2584 public void setJsMessageSet(String messageclass, String viewId,
2585 String[] colcommands)
2587 Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
2590 msgset = new Hashtable<String, String[]>();
2591 jsmessages.put(messageclass, msgset);
2593 msgset.put(viewId, colcommands);
2594 long[] l = new long[colcommands.length];
2595 for (int i = 0; i < colcommands.length; i++)
2597 l[i] = colcommands[i].hashCode();
2599 jshashes.put(messageclass + "|" + viewId, l);
2605 * @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String,
2608 public String getJsMessage(String messageclass, String viewId)
2610 Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
2613 String[] msgs = msgset.get(viewId);
2616 for (int i = 0; i < msgs.length; i++)
2618 if (msgs[i] != null)
2630 public boolean isJsMessageSetChanged(String string, String string2,
2631 String[] colcommands)
2633 long[] l = jshashes.get(string + "|" + string2);
2634 if (l == null && colcommands != null)
2638 for (int i = 0; i < colcommands.length; i++)
2640 if (l[i] != colcommands[i].hashCode())
2648 private Vector jsExecQueue = new Vector();
2650 public Vector getJsExecQueue()
2655 public void setExecutor(JSFunctionExec jsFunctionExec2)
2657 jsFunctionExec = jsFunctionExec2;
2661 * return the given colour value parameter or the given default if parameter
2668 public Color getDefaultColourParameter(String colparam, Color defcolour)
2670 String colprop = getParameter(colparam);
2671 if (colprop == null || colprop.trim().length() == 0)
2675 Color col = jalview.schemes.ColourSchemeProperty
2676 .getAWTColorFromName(colprop);
2681 col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
2682 } catch (Exception ex)
2684 System.err.println("Couldn't parse '" + colprop
2685 + "' as a colour for " + colparam);
2689 return (col == null) ? defcolour : col;
2693 public void openJalviewHelpUrl()
2695 String helpUrl = getParameter("jalviewhelpurl");
2696 if (helpUrl == null || helpUrl.trim().length() < 5)
2698 helpUrl = "http://www.jalview.org/help.html";
2700 showURL(helpUrl, "HELP");
2704 * form a complete URL given a path to a resource and a reference location on
2708 * - an absolute path on the same server as localref or a document
2709 * located relative to localref
2711 * - a URL on the same server as url
2712 * @return a complete URL for the resource located by url
2714 private String resolveUrlForLocalOrAbsolute(String url, URL localref)
2716 String codebase = localref.toString();
2717 if (url.indexOf("/") == 0)
2719 url = codebase.substring(0, codebase.length()
2720 - localref.getFile().length())
2725 url = localref + url;
2731 * open a URL in the browser - resolving it according to relative refs and
2732 * coping with javascript: protocol if necessary.
2737 public void showURL(String url, String target)
2741 if (url.indexOf(":") == -1)
2743 // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
2745 // Should really use docbase, not codebase.
2747 url = resolveUrlForLocalOrAbsolute(
2749 prepend = getDefaultParameter("resolvetocodebase", false) ? getDocumentBase()
2754 .println("Show url (prepended "
2756 + " - toggle resolvetocodebase if code/docbase resolution is wrong): "
2764 System.err.println("Show url: " + url);
2767 if (url.indexOf("javascript:") == 0)
2769 // no target for the javascript context
2770 getAppletContext().showDocument(new java.net.URL(url));
2774 getAppletContext().showDocument(new java.net.URL(url), target);
2776 } catch (Exception ex)
2778 ex.printStackTrace();
2783 * bind structures in a viewer to any matching sequences in an alignFrame (use
2784 * sequenceIds to limit scope of search to specific sequences)
2788 * @param sequenceIds
2789 * @return TODO: consider making an exception structure for indicating when
2790 * binding fails public SequenceStructureBinding
2791 * addStructureViewInstance( AlignFrame alFrame, Object viewer, String
2794 * if (sequenceIds != null && sequenceIds.length() > 0) { return
2795 * alFrame.addStructureViewInstance(viewer,
2796 * separatorListToArray(sequenceIds)); } else { return
2797 * alFrame.addStructureViewInstance(viewer, null); } // return null; }