2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentUtils;
24 import jalview.api.StructureSelectionManagerProvider;
25 import jalview.appletgui.AlignFrame;
26 import jalview.appletgui.AlignViewport;
27 import jalview.appletgui.EmbmenuFrame;
28 import jalview.appletgui.FeatureSettings;
29 import jalview.appletgui.SplitFrame;
30 import jalview.datamodel.Alignment;
31 import jalview.datamodel.AlignmentI;
32 import jalview.datamodel.AlignmentOrder;
33 import jalview.datamodel.ColumnSelection;
34 import jalview.datamodel.HiddenColumns;
35 import jalview.datamodel.PDBEntry;
36 import jalview.datamodel.Sequence;
37 import jalview.datamodel.SequenceGroup;
38 import jalview.datamodel.SequenceI;
39 import jalview.io.AnnotationFile;
40 import jalview.io.AppletFormatAdapter;
41 import jalview.io.DataSourceType;
42 import jalview.io.FileFormatI;
43 import jalview.io.FileFormats;
44 import jalview.io.FileParse;
45 import jalview.io.IdentifyFile;
46 import jalview.io.JPredFile;
47 import jalview.io.JnetAnnotationMaker;
48 import jalview.io.NewickFile;
49 import jalview.javascript.JSFunctionExec;
50 import jalview.javascript.JalviewLiteJsApi;
51 import jalview.javascript.JsCallBack;
52 import jalview.javascript.MouseOverStructureListener;
53 import jalview.structure.SelectionListener;
54 import jalview.structure.StructureSelectionManager;
55 import jalview.util.ColorUtils;
56 import jalview.util.HttpUtils;
57 import jalview.util.MessageManager;
59 import java.applet.Applet;
60 import java.awt.Button;
61 import java.awt.Color;
62 import java.awt.Component;
63 import java.awt.EventQueue;
65 import java.awt.Frame;
66 import java.awt.Graphics;
67 import java.awt.event.ActionEvent;
68 import java.awt.event.WindowAdapter;
69 import java.awt.event.WindowEvent;
70 import java.io.BufferedReader;
71 import java.io.IOException;
72 import java.io.InputStreamReader;
74 import java.util.ArrayList;
75 import java.util.Hashtable;
76 import java.util.List;
77 import java.util.StringTokenizer;
78 import java.util.Vector;
80 import netscape.javascript.JSObject;
83 * Jalview Applet. Runs in Java 1.18 runtime
86 * @version $Revision: 1.92 $
88 public class JalviewLite extends Applet
89 implements StructureSelectionManagerProvider, JalviewLiteJsApi
92 private static final String TRUE = "true";
94 private static final String FALSE = "false";
96 public StructureSelectionManager getStructureSelectionManager()
98 return StructureSelectionManager.getStructureSelectionManager(this);
101 // /////////////////////////////////////////
102 // The following public methods may be called
103 // externally, eg via javascript in HTML page
107 * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences()
110 public String getSelectedSequences()
112 return getSelectedSequencesFrom(getDefaultTargetFrame());
118 * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
121 public String getSelectedSequences(String sep)
123 return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);
130 * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
134 public String getSelectedSequencesFrom(AlignFrame alf)
136 return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);
143 * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
144 * .AlignFrame, java.lang.String)
147 public String getSelectedSequencesFrom(AlignFrame alf, String sep)
149 StringBuffer result = new StringBuffer("");
150 if (sep == null || sep.length() == 0)
152 sep = separator; // "+0x00AC;
154 if (alf.viewport.getSelectionGroup() != null)
156 SequenceI[] seqs = alf.viewport.getSelectionGroup()
157 .getSequencesInOrder(alf.viewport.getAlignment());
159 for (int i = 0; i < seqs.length; i++)
161 result.append(seqs[i].getName());
166 return result.toString();
172 * @see jalview.bin.JalviewLiteJsApi#highlight(java.lang.String,
173 * java.lang.String, java.lang.String)
176 public void highlight(String sequenceId, String position,
177 String alignedPosition)
179 highlightIn(getDefaultTargetFrame(), sequenceId, position,
186 * @see jalview.bin.JalviewLiteJsApi#highlightIn(jalview.appletgui.AlignFrame,
187 * java.lang.String, java.lang.String, java.lang.String)
190 public void highlightIn(final AlignFrame alf, final String sequenceId,
191 final String position, final String alignedPosition)
193 // TODO: could try to highlight in all alignments if alf==null
194 jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
195 alf.viewport.getAlignment().getSequencesArray());
196 final SequenceI sq = matcher.findIdMatch(sequenceId);
202 apos = new Integer(position).intValue();
204 } catch (NumberFormatException ex)
208 final StructureSelectionManagerProvider me = this;
209 final int pos = apos;
210 // use vamsas listener to broadcast to all listeners in scope
211 if (alignedPosition != null && (alignedPosition.trim().length() == 0
212 || alignedPosition.toLowerCase().indexOf("false") > -1))
214 java.awt.EventQueue.invokeLater(new Runnable()
219 StructureSelectionManager.getStructureSelectionManager(me)
220 .mouseOverVamsasSequence(sq, sq.findIndex(pos), null);
226 java.awt.EventQueue.invokeLater(new Runnable()
231 StructureSelectionManager.getStructureSelectionManager(me)
232 .mouseOverVamsasSequence(sq, pos, null);
242 * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
246 public void select(String sequenceIds, String columns)
248 selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator);
254 * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
255 * java.lang.String, java.lang.String)
258 public void select(String sequenceIds, String columns, String sep)
260 selectIn(getDefaultTargetFrame(), sequenceIds, columns, sep);
266 * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
267 * java.lang.String, java.lang.String)
270 public void selectIn(AlignFrame alf, String sequenceIds, String columns)
272 selectIn(alf, sequenceIds, columns, separator);
278 * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
279 * java.lang.String, java.lang.String, java.lang.String)
282 public void selectIn(final AlignFrame alf, String sequenceIds,
283 String columns, String sep)
285 if (sep == null || sep.length() == 0)
293 System.err.println("Selecting region using separator string '"
298 String[] ids = separatorListToArray(sequenceIds, sep);
299 String[] cols = separatorListToArray(columns, sep);
300 final SequenceGroup sel = new SequenceGroup();
301 final ColumnSelection csel = new ColumnSelection();
302 AlignmentI al = alf.viewport.getAlignment();
303 jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
304 alf.viewport.getAlignment().getSequencesArray());
305 int start = 0, end = al.getWidth(), alw = al.getWidth();
306 boolean seqsfound = true;
307 if (ids != null && ids.length > 0)
310 for (int i = 0; i < ids.length; i++)
312 if (ids[i].trim().length() == 0)
316 SequenceI sq = matcher.findIdMatch(ids[i]);
320 sel.addSequence(sq, false);
324 boolean inseqpos = false;
325 if (cols != null && cols.length > 0)
327 boolean seset = false;
328 for (int i = 0; i < cols.length; i++)
330 String cl = cols[i].trim();
331 if (cl.length() == 0)
336 if ((p = cl.indexOf("-")) > -1)
338 int from = -1, to = -1;
341 from = new Integer(cl.substring(0, p)).intValue();
343 } catch (NumberFormatException ex)
346 "ERROR: Couldn't parse first integer in range element column selection string '"
347 + cl + "' - format is 'from-to'");
352 to = new Integer(cl.substring(p + 1)).intValue();
354 } catch (NumberFormatException ex)
357 "ERROR: Couldn't parse second integer in range element column selection string '"
358 + cl + "' - format is 'from-to'");
361 if (from >= 0 && to >= 0)
378 // comment to prevent range extension
388 for (int r = from; r <= to; r++)
390 if (r >= 0 && r < alw)
397 System.err.println("Range '" + cl + "' deparsed as [" + from
403 System.err.println("ERROR: Invalid Range '" + cl
404 + "' deparsed as [" + from + "," + to + "]");
412 r = new Integer(cl).intValue();
414 } catch (NumberFormatException ex)
416 if (cl.toLowerCase().equals("sequence"))
418 // we are in the dataset sequence's coordinate frame.
424 "ERROR: Couldn't parse integer from point selection element of column selection string '"
429 if (r >= 0 && r <= alw)
439 // comment to prevent range extension
452 System.err.println("Point selection '" + cl
453 + "' deparsed as [" + r + "]");
458 System.err.println("ERROR: Invalid Point selection '" + cl
459 + "' deparsed as [" + r + "]");
466 // we only propagate the selection when it was the null selection, or the
467 // given sequences were found in the alignment.
468 if (inseqpos && sel.getSize() > 0)
470 // assume first sequence provides reference frame ?
471 SequenceI rs = sel.getSequenceAt(0);
472 start = rs.findIndex(start);
473 end = rs.findIndex(end);
474 List<Integer> cs = new ArrayList<Integer>(csel.getSelected());
476 for (Integer selectedCol : cs)
478 csel.addElement(rs.findIndex(selectedCol));
481 sel.setStartRes(start);
483 EventQueue.invokeLater(new Runnable()
488 alf.select(sel, csel,
489 alf.getAlignViewport().getAlignment().getHiddenColumns());
499 * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignment(java.lang.
500 * String, java.lang.String)
503 public String getSelectedSequencesAsAlignment(String format,
506 return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(),
514 * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignmentFrom(jalview
515 * .appletgui.AlignFrame, java.lang.String, java.lang.String)
518 public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
519 String format, String suffix)
523 FileFormatI theFormat = FileFormats.getInstance().forName(format);
524 boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
525 if (alf.viewport.getSelectionGroup() != null)
527 // JBPNote: getSelectionAsNewSequence behaviour has changed - this
528 // method now returns a full copy of sequence data
529 // TODO consider using getSequenceSelection instead here
530 String reply = new AppletFormatAdapter().formatSequences(theFormat,
531 new Alignment(alf.viewport.getSelectionAsNewSequence()),
535 } catch (IllegalArgumentException ex)
537 ex.printStackTrace();
538 return "Error retrieving alignment, possibly invalid format specifier: "
547 * @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder()
550 public String getAlignmentOrder()
552 return getAlignmentOrderFrom(getDefaultTargetFrame());
559 * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
563 public String getAlignmentOrderFrom(AlignFrame alf)
565 return getAlignmentOrderFrom(alf, separator);
572 * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
573 * , java.lang.String)
576 public String getAlignmentOrderFrom(AlignFrame alf, String sep)
578 AlignmentI alorder = alf.getAlignViewport().getAlignment();
579 String[] order = new String[alorder.getHeight()];
580 for (int i = 0; i < order.length; i++)
582 order[i] = alorder.getSequenceAt(i).getName();
584 return arrayToSeparatorList(order);
590 * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
594 public String orderBy(String order, String undoName)
596 return orderBy(order, undoName, separator);
602 * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
603 * java.lang.String, java.lang.String)
606 public String orderBy(String order, String undoName, String sep)
608 return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep);
615 * jalview.bin.JalviewLiteJsApi#orderAlignmentBy(jalview.appletgui.AlignFrame,
616 * java.lang.String, java.lang.String, java.lang.String)
619 public String orderAlignmentBy(AlignFrame alf, String order,
620 String undoName, String sep)
622 String[] ids = separatorListToArray(order, sep);
623 SequenceI[] sqs = null;
624 if (ids != null && ids.length > 0)
626 jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
627 alf.viewport.getAlignment().getSequencesArray());
629 sqs = new SequenceI[ids.length];
630 for (int i = 0; i < ids.length; i++)
632 if (ids[i].trim().length() == 0)
636 SequenceI sq = matcher.findIdMatch(ids[i]);
644 SequenceI[] sqq = new SequenceI[s];
645 System.arraycopy(sqs, 0, sqq, 0, s);
658 final AlignmentOrder aorder = new AlignmentOrder(sqs);
660 if (undoName != null && undoName.trim().length() == 0)
664 final String _undoName = undoName;
665 // TODO: deal with synchronization here: cannot raise any events until after
666 // this has returned.
667 return alf.sortBy(aorder, _undoName) ? TRUE : "";
673 * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String)
676 public String getAlignment(String format)
678 return getAlignmentFrom(getDefaultTargetFrame(), format, TRUE);
685 * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
689 public String getAlignmentFrom(AlignFrame alf, String format)
691 return getAlignmentFrom(alf, format, TRUE);
697 * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String,
701 public String getAlignment(String format, String suffix)
703 return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);
710 * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
711 * java.lang.String, java.lang.String)
714 public String getAlignmentFrom(AlignFrame alf, String format,
719 boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
721 FileFormatI theFormat = FileFormats.getInstance().forName(format);
722 String reply = new AppletFormatAdapter().formatSequences(theFormat,
723 alf.viewport.getAlignment(), seqlimits);
725 } catch (IllegalArgumentException ex)
727 ex.printStackTrace();
728 return "Error retrieving alignment, possibly invalid format specifier: "
736 * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
739 public void loadAnnotation(String annotation)
741 loadAnnotationFrom(getDefaultTargetFrame(), annotation);
748 * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
749 * , java.lang.String)
752 public void loadAnnotationFrom(AlignFrame alf, String annotation)
754 if (new AnnotationFile().annotateAlignmentView(alf.getAlignViewport(),
755 annotation, DataSourceType.PASTE))
757 alf.alignPanel.fontChanged();
758 alf.alignPanel.setScrollValues(0, 0);
762 alf.parseFeaturesFile(annotation, DataSourceType.PASTE);
769 * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
772 public void loadFeatures(String features, boolean autoenabledisplay)
774 loadFeaturesFrom(getDefaultTargetFrame(), features, autoenabledisplay);
781 * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
782 * , java.lang.String)
785 public boolean loadFeaturesFrom(AlignFrame alf, String features,
786 boolean autoenabledisplay)
788 return alf.parseFeaturesFile(features, DataSourceType.PASTE,
795 * @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String)
798 public String getFeatures(String format)
800 return getFeaturesFrom(getDefaultTargetFrame(), format);
807 * jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame,
811 public String getFeaturesFrom(AlignFrame alf, String format)
813 return alf.outputFeatures(false, format);
819 * @see jalview.bin.JalviewLiteJsApi#getAnnotation()
822 public String getAnnotation()
824 return getAnnotationFrom(getDefaultTargetFrame());
831 * jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame
835 public String getAnnotationFrom(AlignFrame alf)
837 return alf.outputAnnotations(false);
843 * @see jalview.bin.JalviewLiteJsApi#newView()
846 public AlignFrame newView()
848 return newViewFrom(getDefaultTargetFrame());
854 * @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String)
857 public AlignFrame newView(String name)
859 return newViewFrom(getDefaultTargetFrame(), name);
865 * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame)
868 public AlignFrame newViewFrom(AlignFrame alf)
870 return alf.newView(null);
876 * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame,
880 public AlignFrame newViewFrom(AlignFrame alf, String name)
882 return alf.newView(name);
888 * @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String,
892 public AlignFrame loadAlignment(String text, String title)
894 AlignmentI al = null;
898 FileFormatI format = new IdentifyFile().identify(text,
899 DataSourceType.PASTE);
900 al = new AppletFormatAdapter().readFile(text, DataSourceType.PASTE,
902 if (al.getHeight() > 0)
904 return new AlignFrame(al, this, title, false);
906 } catch (IOException ex)
908 ex.printStackTrace();
916 * @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String)
919 public void setMouseoverListener(String listener)
921 setMouseoverListener(currentAlignFrame, listener);
924 private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<jalview.javascript.JSFunctionExec>();
930 * jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame
931 * , java.lang.String)
934 public void setMouseoverListener(AlignFrame af, String listener)
936 if (listener != null)
938 listener = listener.trim();
939 if (listener.length() == 0)
942 "jalview Javascript error: Ignoring empty function for mouseover listener.");
946 jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener(
948 javascriptListeners.addElement(mol);
949 StructureSelectionManager.getStructureSelectionManager(this)
950 .addStructureViewerListener(mol);
953 System.err.println("Added a mouseover listener for "
954 + ((af == null) ? "All frames"
956 + af.getAlignViewport().getSequenceSetId()));
957 System.err.println("There are now " + javascriptListeners.size()
958 + " listeners in total.");
965 * @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String)
968 public void setSelectionListener(String listener)
970 setSelectionListener(null, listener);
977 * jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame
978 * , java.lang.String)
981 public void setSelectionListener(AlignFrame af, String listener)
983 if (listener != null)
985 listener = listener.trim();
986 if (listener.length() == 0)
989 "jalview Javascript error: Ignoring empty function for selection listener.");
993 jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender(
995 javascriptListeners.addElement(mol);
996 StructureSelectionManager.getStructureSelectionManager(this)
997 .addSelectionListener(mol);
1000 System.err.println("Added a selection listener for "
1001 + ((af == null) ? "All frames"
1003 + af.getAlignViewport().getSequenceSetId()));
1004 System.err.println("There are now " + javascriptListeners.size()
1005 + " listeners in total.");
1010 * Callable from javascript to register a javascript function to pass events
1011 * to a structure viewer.
1014 * the name of a javascript function
1016 * a token separated list of PDB file names listened for
1017 * @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String,
1021 public void setStructureListener(String listener, String modelSet)
1023 if (listener != null)
1025 listener = listener.trim();
1026 if (listener.length() == 0)
1029 "jalview Javascript error: Ignoring empty function for selection listener.");
1033 MouseOverStructureListener mol = new MouseOverStructureListener(this,
1034 listener, separatorListToArray(modelSet));
1035 javascriptListeners.addElement(mol);
1036 StructureSelectionManager.getStructureSelectionManager(this)
1037 .addStructureViewerListener(mol);
1040 System.err.println("Added a javascript structure viewer listener '"
1042 System.err.println("There are now " + javascriptListeners.size()
1043 + " listeners in total.");
1051 * jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui
1052 * .AlignFrame, java.lang.String)
1055 public void removeJavascriptListener(AlignFrame af, String listener)
1057 if (listener != null)
1059 listener = listener.trim();
1060 if (listener.length() == 0)
1065 boolean rprt = false;
1066 for (int ms = 0, msSize = javascriptListeners.size(); ms < msSize;)
1068 Object lstn = javascriptListeners.elementAt(ms);
1069 JsCallBack lstner = (JsCallBack) lstn;
1070 if ((af == null || lstner.getAlignFrame() == af) && (listener == null
1071 || lstner.getListenerFunction().equals(listener)))
1073 javascriptListeners.removeElement(lstner);
1075 if (lstner instanceof SelectionListener)
1077 StructureSelectionManager.getStructureSelectionManager(this)
1078 .removeSelectionListener((SelectionListener) lstner);
1082 StructureSelectionManager.getStructureSelectionManager(this)
1083 .removeStructureViewerListener(lstner, null);
1088 System.err.println("Removed listener '" + listener + "'");
1098 System.err.println("There are now " + javascriptListeners.size()
1099 + " listeners in total.");
1106 System.err.println("Applet " + getName() + " stop().");
1111 public void destroy()
1113 System.err.println("Applet " + getName() + " destroy().");
1117 private void tidyUp()
1120 if (currentAlignFrame != null && currentAlignFrame.viewport != null
1121 && currentAlignFrame.viewport.applet != null)
1123 AlignViewport av = currentAlignFrame.viewport;
1124 currentAlignFrame.closeMenuItem_actionPerformed();
1126 currentAlignFrame = null;
1128 if (javascriptListeners != null)
1130 while (javascriptListeners.size() > 0)
1132 jalview.javascript.JSFunctionExec mol = javascriptListeners
1134 javascriptListeners.removeElement(mol);
1135 if (mol instanceof SelectionListener)
1137 StructureSelectionManager.getStructureSelectionManager(this)
1138 .removeSelectionListener((SelectionListener) mol);
1142 StructureSelectionManager.getStructureSelectionManager(this)
1143 .removeStructureViewerListener(mol, null);
1148 if (jsFunctionExec != null)
1150 jsFunctionExec.stopQueue();
1151 jsFunctionExec.jvlite = null;
1153 initialAlignFrame = null;
1154 jsFunctionExec = null;
1155 javascriptListeners = null;
1156 StructureSelectionManager.release(this);
1159 private jalview.javascript.JSFunctionExec jsFunctionExec;
1164 * @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String,
1165 * java.lang.String, java.lang.String)
1168 public void mouseOverStructure(final String pdbResNum, final String chain,
1169 final String pdbfile)
1171 final StructureSelectionManagerProvider me = this;
1172 java.awt.EventQueue.invokeLater(new Runnable()
1179 StructureSelectionManager.getStructureSelectionManager(me)
1180 .mouseOverStructure(new Integer(pdbResNum).intValue(),
1185 .println("mouseOver for '" + pdbResNum + "' in chain '"
1186 + chain + "' in structure '" + pdbfile + "'");
1188 } catch (NumberFormatException e)
1190 System.err.println("Ignoring invalid residue number string '"
1202 * jalview.bin.JalviewLiteJsApi#scrollViewToIn(jalview.appletgui.AlignFrame,
1203 * java.lang.String, java.lang.String)
1206 public void scrollViewToIn(final AlignFrame alf, final String topRow,
1207 final String leftHandColumn)
1209 java.awt.EventQueue.invokeLater(new Runnable()
1216 alf.scrollTo(new Integer(topRow).intValue(),
1217 new Integer(leftHandColumn).intValue());
1219 } catch (Exception ex)
1221 System.err.println("Couldn't parse integer arguments (topRow='"
1222 + topRow + "' and leftHandColumn='" + leftHandColumn
1224 ex.printStackTrace();
1234 * jalview.javascript.JalviewLiteJsApi#scrollViewToRowIn(jalview.appletgui
1235 * .AlignFrame, java.lang.String)
1238 public void scrollViewToRowIn(final AlignFrame alf, final String topRow)
1241 java.awt.EventQueue.invokeLater(new Runnable()
1248 alf.scrollToRow(new Integer(topRow).intValue());
1250 } catch (Exception ex)
1252 System.err.println("Couldn't parse integer arguments (topRow='"
1254 ex.printStackTrace();
1265 * jalview.javascript.JalviewLiteJsApi#scrollViewToColumnIn(jalview.appletgui
1266 * .AlignFrame, java.lang.String)
1269 public void scrollViewToColumnIn(final AlignFrame alf,
1270 final String leftHandColumn)
1272 java.awt.EventQueue.invokeLater(new Runnable()
1280 alf.scrollToColumn(new Integer(leftHandColumn).intValue());
1282 } catch (Exception ex)
1285 "Couldn't parse integer arguments (leftHandColumn='"
1286 + leftHandColumn + "')");
1287 ex.printStackTrace();
1294 // //////////////////////////////////////////////
1295 // //////////////////////////////////////////////
1297 public static int lastFrameX = 200;
1299 public static int lastFrameY = 200;
1301 boolean fileFound = true;
1303 String file = "No file";
1305 String file2 = null;
1307 Button launcher = new Button(
1308 MessageManager.getString("label.start_jalview"));
1311 * The currentAlignFrame is static, it will change if and when the user
1312 * selects a new window. Note that it will *never* point back to the embedded
1313 * AlignFrame if the applet is started as embedded on the page and then
1314 * afterwards a new view is created.
1316 public AlignFrame currentAlignFrame = null;
1319 * This is the first frame to be displayed, and does not change. API calls
1320 * will default to this instance if currentAlignFrame is null.
1322 AlignFrame initialAlignFrame = null;
1324 boolean embedded = false;
1326 private boolean checkForJmol = true;
1328 private boolean checkedForJmol = false; // ensure we don't check for jmol
1330 // every time the app is re-inited
1332 public boolean jmolAvailable = false;
1334 private boolean alignPdbStructures = false;
1337 * use an external structure viewer exclusively (no jmols or MCViews will be
1338 * opened by JalviewLite itself)
1340 public boolean useXtrnalSviewer = false;
1342 public static boolean debug = false;
1344 static String builddate = null, version = null, installation = null;
1346 private static void initBuildDetails()
1348 if (builddate == null)
1350 builddate = "unknown";
1352 installation = "applet";
1353 java.net.URL url = JalviewLite.class
1354 .getResource("/.build_properties");
1359 BufferedReader reader = new BufferedReader(
1360 new InputStreamReader(url.openStream()));
1362 while ((line = reader.readLine()) != null)
1364 if (line.indexOf("VERSION") > -1)
1366 version = line.substring(line.indexOf("=") + 1);
1368 if (line.indexOf("BUILD_DATE") > -1)
1370 builddate = line.substring(line.indexOf("=") + 1);
1372 if (line.indexOf("INSTALLATION") > -1)
1374 installation = line.substring(line.indexOf("=") + 1);
1377 } catch (Exception ex)
1379 ex.printStackTrace();
1385 public static String getBuildDate()
1391 public static String getInstallation()
1394 return installation;
1397 public static String getVersion()
1403 // public JSObject scriptObject = null;
1406 * init method for Jalview Applet
1411 debug = TRUE.equalsIgnoreCase(getParameter("debug"));
1416 System.err.println("Applet context is '"
1417 + getAppletContext().getClass().toString() + "'");
1419 JSObject scriptObject = JSObject.getWindow(this);
1420 if (debug && scriptObject != null)
1422 System.err.println("Applet has Javascript callback support.");
1425 } catch (Exception ex)
1428 "Warning: No JalviewLite javascript callbacks available.");
1431 ex.printStackTrace();
1437 System.err.println("JalviewLite Version " + getVersion());
1438 System.err.println("Build Date : " + getBuildDate());
1439 System.err.println("Installation : " + getInstallation());
1441 String externalsviewer = getParameter("externalstructureviewer");
1442 if (externalsviewer != null)
1444 useXtrnalSviewer = externalsviewer.trim().toLowerCase().equals(TRUE);
1447 * if true disable the check for jmol
1449 String chkforJmol = getParameter("nojmol");
1450 if (chkforJmol != null)
1452 checkForJmol = !chkforJmol.equals(TRUE);
1455 * get the separator parameter if present
1457 String sep = getParameter("separator");
1460 if (sep.length() > 0)
1465 System.err.println("Separator set to '" + separator + "'");
1470 throw new Error(MessageManager
1471 .getString("error.invalid_separator_parameter"));
1477 String param = getParameter("RGB");
1483 r = Integer.parseInt(param.substring(0, 2), 16);
1484 g = Integer.parseInt(param.substring(2, 4), 16);
1485 b = Integer.parseInt(param.substring(4, 6), 16);
1486 } catch (Exception ex)
1493 param = getParameter("label");
1496 launcher.setLabel(param);
1499 setBackground(new Color(r, g, b));
1501 file = getParameter("file");
1505 // Maybe the sequences are added as parameters
1506 StringBuffer data = new StringBuffer("PASTE");
1508 while ((file = getParameter("sequence" + i)) != null)
1510 data.append(file.toString() + "\n");
1513 if (data.length() > 5)
1515 file = data.toString();
1518 if (getDefaultParameter("enableSplitFrame", true))
1520 file2 = getParameter("file2");
1523 embedded = TRUE.equalsIgnoreCase(getParameter("embedded"));
1526 LoadingThread loader = new LoadingThread(file, file2, this);
1529 else if (file != null)
1532 * Start the applet immediately or show a button to start it
1534 if (FALSE.equalsIgnoreCase(getParameter("showbutton")))
1536 LoadingThread loader = new LoadingThread(file, file2, this);
1542 launcher.addActionListener(new java.awt.event.ActionListener()
1545 public void actionPerformed(ActionEvent e)
1547 LoadingThread loader = new LoadingThread(file, file2,
1556 // jalview initialisation with no alignment. loadAlignment() method can
1557 // still be called to open new alignments.
1564 private void initLiveConnect()
1566 // try really hard to get the liveConnect thing working
1567 boolean notFailed = false;
1569 while (!notFailed && tries < 10)
1573 System.err.println("LiveConnect request thread going to sleep.");
1577 Thread.sleep(700 * (1 + tries));
1578 } catch (InterruptedException q)
1584 System.err.println("LiveConnect request thread woken up.");
1588 JSObject scriptObject = JSObject.getWindow(this);
1589 if (scriptObject.eval("navigator") != null)
1593 } catch (Exception jsex)
1595 System.err.println("Attempt " + tries
1596 + " to access LiveConnect javascript failed.");
1601 private void callInitCallback()
1603 String initjscallback = getParameter("oninit");
1604 if (initjscallback == null)
1608 initjscallback = initjscallback.trim();
1609 if (initjscallback.length() > 0)
1611 JSObject scriptObject = null;
1614 scriptObject = JSObject.getWindow(this);
1615 } catch (Exception ex)
1619 // try really hard to let the browser plugin know we want liveconnect
1622 if (scriptObject != null)
1626 // do onInit with the JS executor thread
1627 new JSFunctionExec(this).executeJavascriptFunction(true,
1628 initjscallback, null,
1629 "Calling oninit callback '" + initjscallback + "'.");
1630 } catch (Exception e)
1632 System.err.println("Exception when executing _oninit callback '"
1633 + initjscallback + "'.");
1634 e.printStackTrace();
1639 System.err.println("Not executing _oninit callback '"
1640 + initjscallback + "' - no scripting allowed.");
1646 * Initialises and displays a new java.awt.Frame
1649 * java.awt.Frame to be displayed
1651 * title of new frame
1653 * width if new frame
1655 * height of new frame
1657 public static void addFrame(final Frame frame, String title, int width,
1660 frame.setLocation(lastFrameX, lastFrameY);
1663 frame.setSize(width, height);
1664 frame.setTitle(title);
1665 frame.addWindowListener(new WindowAdapter()
1668 public void windowClosing(WindowEvent e)
1670 if (frame instanceof AlignFrame)
1672 AlignViewport vp = ((AlignFrame) frame).viewport;
1673 ((AlignFrame) frame).closeMenuItem_actionPerformed();
1674 if (vp.applet.currentAlignFrame == frame)
1676 vp.applet.currentAlignFrame = null;
1684 if (frame instanceof EmbmenuFrame)
1686 ((EmbmenuFrame) frame).destroyMenus();
1688 frame.setMenuBar(null);
1693 public void windowActivated(WindowEvent e)
1695 if (frame instanceof AlignFrame)
1697 ((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame;
1700 System.err.println("Activated window " + frame);
1704 super.windowActivated(e);
1707 * Probably not necessary to do this - see TODO above. (non-Javadoc)
1710 * java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent
1713 * public void windowDeactivated(WindowEvent e) { if (currentAlignFrame ==
1714 * frame) { currentAlignFrame = null; if (debug) {
1715 * System.err.println("Deactivated window "+frame); } }
1716 * super.windowDeactivated(e); }
1719 frame.setVisible(true);
1723 * This paints the background surrounding the "Launch Jalview button" <br>
1725 * If file given in parameter not found, displays error message
1731 public void paint(Graphics g)
1735 g.setColor(new Color(200, 200, 200));
1736 g.setColor(Color.cyan);
1737 g.fillRect(0, 0, getSize().width, getSize().height);
1738 g.setColor(Color.red);
1740 MessageManager.getString("label.jalview_cannot_open_file"), 5,
1742 g.drawString("\"" + file + "\"", 5, 30);
1746 g.setColor(Color.black);
1747 g.setFont(new Font("Arial", Font.BOLD, 24));
1748 g.drawString(MessageManager.getString("label.jalview_applet"), 50,
1749 getSize().height / 2 - 30);
1750 g.drawString(MessageManager.getString("label.loading_data") + "...",
1751 50, getSize().height / 2);
1756 * get all components associated with the applet of the given type
1761 public Vector getAppletWindow(Class class1)
1763 Vector wnds = new Vector();
1764 Component[] cmp = getComponents();
1767 for (int i = 0; i < cmp.length; i++)
1769 if (class1.isAssignableFrom(cmp[i].getClass()))
1771 wnds.addElement(cmp);
1778 class LoadJmolThread extends Thread
1780 private boolean running = false;
1785 if (running || checkedForJmol)
1794 if (!System.getProperty("java.version").startsWith("1.1"))
1796 Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
1797 jmolAvailable = true;
1802 "Jmol not available - Using MCview for structures");
1804 } catch (java.lang.ClassNotFoundException ex)
1810 jmolAvailable = false;
1814 "Skipping Jmol check. Will use MCView (probably)");
1817 checkedForJmol = true;
1821 public boolean notFinished()
1823 return running || !checkedForJmol;
1827 class LoadingThread extends Thread
1830 * State variable: protocol for access to file source
1832 DataSourceType protocol;
1834 String _file; // alignment file or URL spec
1836 String _file2; // second alignment file or URL spec
1840 private void dbgMsg(String msg)
1842 if (JalviewLite.debug)
1844 System.err.println(msg);
1849 * update the protocol state variable for accessing the datasource located
1853 * @return possibly updated datasource string
1855 public String resolveFileProtocol(String path)
1860 if (path.startsWith("PASTE"))
1862 protocol = DataSourceType.PASTE;
1863 return path.substring(5);
1869 if (path.indexOf("://") != -1)
1871 protocol = DataSourceType.URL;
1876 * try relative to document root
1878 URL documentBase = getDocumentBase();
1879 String withDocBase = resolveUrlForLocalOrAbsolute(path, documentBase);
1880 if (HttpUtils.isValidUrl(withDocBase))
1884 System.err.println("Prepended document base '" + documentBase
1885 + "' to make: '" + withDocBase + "'");
1887 protocol = DataSourceType.URL;
1892 * try relative to codebase (if different to document base)
1894 URL codeBase = getCodeBase();
1895 String withCodeBase = applet.resolveUrlForLocalOrAbsolute(path,
1897 if (!withCodeBase.equals(withDocBase)
1898 && HttpUtils.isValidUrl(withCodeBase))
1900 protocol = DataSourceType.URL;
1903 System.err.println("Prepended codebase '" + codeBase
1904 + "' to make: '" + withCodeBase + "'");
1906 return withCodeBase;
1910 * try locating by classloader; try this last so files in the directory
1911 * are resolved using document base
1913 if (inArchive(path))
1915 protocol = DataSourceType.CLASSLOADER;
1920 public LoadingThread(String file, String file2, JalviewLite _applet)
1923 this._file2 = file2;
1930 LoadJmolThread jmolchecker = new LoadJmolThread();
1931 jmolchecker.start();
1932 while (jmolchecker.notFinished())
1934 // wait around until the Jmol check is complete.
1938 } catch (Exception e)
1943 // applet.callInitCallback();
1947 * Load the alignment and any related files as specified by applet
1950 private void startLoading()
1952 dbgMsg("Loading thread started with:\n>>file\n" + _file
1955 dbgMsg("Loading started.");
1957 AlignFrame newAlignFrame = readAlignment(_file);
1958 AlignFrame newAlignFrame2 = readAlignment(_file2);
1959 if (newAlignFrame != null)
1961 addToDisplay(newAlignFrame, newAlignFrame2);
1962 loadTree(newAlignFrame);
1964 loadScoreFile(newAlignFrame);
1966 loadFeatures(newAlignFrame);
1968 loadAnnotations(newAlignFrame);
1970 loadJnetFile(newAlignFrame);
1972 loadPdbFiles(newAlignFrame);
1977 applet.remove(launcher);
1984 * Add an AlignFrame to the display; or if two are provided, a SplitFrame.
1989 public void addToDisplay(AlignFrame af, AlignFrame af2)
1993 AlignmentI al1 = af.viewport.getAlignment();
1994 AlignmentI al2 = af2.viewport.getAlignment();
1995 AlignmentI cdna = al1.isNucleotide() ? al1 : al2;
1996 AlignmentI prot = al1.isNucleotide() ? al2 : al1;
1997 if (AlignmentUtils.mapProteinAlignmentToCdna(prot, cdna))
2000 SplitFrame sf = new SplitFrame(af, af2);
2001 sf.addToDisplay(embedded, JalviewLite.this);
2006 String msg = "Could not map any sequence in " + af2.getTitle()
2008 + (al1.isNucleotide() ? "protein product" : "cDNA")
2009 + " for " + af.getTitle();
2010 System.err.println(msg);
2014 af.addToDisplay(embedded);
2018 * Read the alignment file (from URL, text 'paste', or archive by
2023 protected AlignFrame readAlignment(String fileParam)
2025 if (fileParam == null)
2029 String resolvedFile = resolveFileProtocol(fileParam);
2030 AlignmentI al = null;
2033 FileFormatI format = new IdentifyFile().identify(resolvedFile,
2035 dbgMsg("File identified as '" + format + "'");
2036 al = new AppletFormatAdapter().readFile(resolvedFile, protocol,
2038 if ((al != null) && (al.getHeight() > 0))
2040 dbgMsg("Successfully loaded file.");
2041 al.setDataset(null);
2042 AlignFrame newAlignFrame = new AlignFrame(al, applet,
2043 resolvedFile, embedded, false);
2044 newAlignFrame.setTitle(resolvedFile);
2045 if (initialAlignFrame == null)
2047 initialAlignFrame = newAlignFrame;
2049 // update the focus.
2050 currentAlignFrame = newAlignFrame;
2052 if (protocol == DataSourceType.PASTE)
2054 newAlignFrame.setTitle(MessageManager
2055 .formatMessage("label.sequences_from", new Object[]
2056 { applet.getDocumentBase().toString() }));
2059 newAlignFrame.statusBar.setText(MessageManager.formatMessage(
2060 "label.successfully_loaded_file", new Object[]
2063 return newAlignFrame;
2065 } catch (java.io.IOException ex)
2067 dbgMsg("File load exception.");
2068 ex.printStackTrace();
2073 FileParse fp = new FileParse(resolvedFile, protocol);
2075 dbgMsg(">>>Dumping contents of '" + resolvedFile + "' " + "("
2077 while ((ln = fp.nextLine()) != null)
2081 dbgMsg(">>>Dump finished.");
2082 } catch (Exception e)
2085 "Exception when trying to dump the content of the file parameter.");
2086 e.printStackTrace();
2094 * Load PDBFiles if any specified by parameter(s). Returns true if loaded,
2100 protected boolean loadPdbFiles(AlignFrame alignFrame)
2102 boolean result = false;
2104 * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6 -
2105 * related to JAL-434
2108 applet.setAlignPdbStructures(
2109 getDefaultParameter("alignpdbfiles", false));
2111 * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
2114 * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
2116 * <param name="PDBfile3" value="1q0o Q45135_9MICO">
2119 int pdbFileCount = 0;
2120 // Accumulate pdbs here if they are heading for the same view (if
2121 // alignPdbStructures is true)
2122 Vector pdbs = new Vector();
2123 // create a lazy matcher if we're asked to
2124 jalview.analysis.SequenceIdMatcher matcher = (applet
2125 .getDefaultParameter("relaxedidmatch", false))
2126 ? new jalview.analysis.SequenceIdMatcher(
2127 alignFrame.getAlignViewport().getAlignment()
2128 .getSequencesArray())
2134 if (pdbFileCount > 0)
2136 param = applet.getParameter("PDBFILE" + pdbFileCount);
2140 param = applet.getParameter("PDBFILE");
2145 PDBEntry pdb = new PDBEntry();
2148 SequenceI[] seqs = null;
2149 String[] chains = null;
2151 StringTokenizer st = new StringTokenizer(param, " ");
2153 if (st.countTokens() < 2)
2155 String sequence = applet.getParameter("PDBSEQ");
2156 if (sequence != null)
2158 seqs = new SequenceI[] { matcher == null
2159 ? (Sequence) alignFrame.getAlignViewport()
2160 .getAlignment().findName(sequence)
2161 : matcher.findIdMatch(sequence) };
2167 param = st.nextToken();
2168 List<SequenceI> tmp = new ArrayList<SequenceI>();
2169 List<String> tmp2 = new ArrayList<String>();
2171 while (st.hasMoreTokens())
2173 seqstring = st.nextToken();
2174 StringTokenizer st2 = new StringTokenizer(seqstring, "=");
2175 if (st2.countTokens() > 1)
2177 // This is the chain
2178 tmp2.add(st2.nextToken());
2179 seqstring = st2.nextToken();
2181 tmp.add(matcher == null
2182 ? (Sequence) alignFrame.getAlignViewport()
2183 .getAlignment().findName(seqstring)
2184 : matcher.findIdMatch(seqstring));
2187 seqs = tmp.toArray(new SequenceI[tmp.size()]);
2188 if (tmp2.size() == tmp.size())
2190 chains = tmp2.toArray(new String[tmp2.size()]);
2193 param = resolveFileProtocol(param);
2194 // TODO check JAL-357 for files in a jar (CLASSLOADER)
2199 for (int i = 0; i < seqs.length; i++)
2201 if (seqs[i] != null)
2203 ((Sequence) seqs[i]).addPDBId(pdb);
2204 StructureSelectionManager
2205 .getStructureSelectionManager(applet)
2206 .registerPDBEntry(pdb);
2210 if (JalviewLite.debug)
2212 // this may not really be a problem but we give a warning
2215 "Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
2221 if (!alignPdbStructures)
2223 alignFrame.newStructureView(applet, pdb, seqs, chains,
2228 pdbs.addElement(new Object[] { pdb, seqs, chains, protocol });
2234 } while (param != null || pdbFileCount < 10);
2235 if (pdbs.size() > 0)
2237 SequenceI[][] seqs = new SequenceI[pdbs.size()][];
2238 PDBEntry[] pdb = new PDBEntry[pdbs.size()];
2239 String[][] chains = new String[pdbs.size()][];
2240 String[] protocols = new String[pdbs.size()];
2241 for (int pdbsi = 0, pdbsiSize = pdbs
2242 .size(); pdbsi < pdbsiSize; pdbsi++)
2244 Object[] o = (Object[]) pdbs.elementAt(pdbsi);
2245 pdb[pdbsi] = (PDBEntry) o[0];
2246 seqs[pdbsi] = (SequenceI[]) o[1];
2247 chains[pdbsi] = (String[]) o[2];
2248 protocols[pdbsi] = (String) o[3];
2250 alignFrame.alignedStructureView(applet, pdb, seqs, chains,
2258 * Load in a Jnetfile if specified by parameter. Returns true if loaded,
2264 protected boolean loadJnetFile(AlignFrame alignFrame)
2266 boolean result = false;
2267 String param = applet.getParameter("jnetfile");
2270 // jnet became jpred around 2016
2271 param = applet.getParameter("jpredfile");
2277 param = resolveFileProtocol(param);
2278 JPredFile predictions = new JPredFile(param, protocol);
2279 JnetAnnotationMaker.add_annotation(predictions,
2280 alignFrame.viewport.getAlignment(), 0, false);
2281 // false == do not add sequence profile from concise output
2282 SequenceI repseq = alignFrame.viewport.getAlignment()
2284 alignFrame.viewport.getAlignment().setSeqrep(repseq);
2285 HiddenColumns cs = new HiddenColumns();
2286 cs.hideInsertionsFor(repseq);
2287 alignFrame.viewport.getAlignment().setHiddenColumns(cs);
2288 alignFrame.alignPanel.fontChanged();
2289 alignFrame.alignPanel.setScrollValues(0, 0);
2291 } catch (Exception ex)
2293 ex.printStackTrace();
2300 * Load annotations if specified by parameter. Returns true if loaded, else
2306 protected boolean loadAnnotations(AlignFrame alignFrame)
2308 boolean result = false;
2309 String param = applet.getParameter("annotations");
2312 param = resolveFileProtocol(param);
2314 if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
2317 alignFrame.alignPanel.fontChanged();
2318 alignFrame.alignPanel.setScrollValues(0, 0);
2324 "Annotations were not added from annotation file '"
2332 * Load features file and view settings as specified by parameters. Returns
2333 * true if features were loaded, else false.
2338 protected boolean loadFeatures(AlignFrame alignFrame)
2340 boolean result = false;
2341 // ///////////////////////////
2342 // modify display of features
2343 // we do this before any features have been loaded, ensuring any hidden
2344 // groups are hidden when features first displayed
2346 // hide specific groups
2348 String param = applet.getParameter("hidefeaturegroups");
2351 alignFrame.setFeatureGroupState(separatorListToArray(param), false);
2352 // applet.setFeatureGroupStateOn(newAlignFrame, param, false);
2354 // show specific groups
2355 param = applet.getParameter("showfeaturegroups");
2358 alignFrame.setFeatureGroupState(separatorListToArray(param), true);
2359 // applet.setFeatureGroupStateOn(newAlignFrame, param, true);
2361 // and now load features
2362 param = applet.getParameter("features");
2365 param = resolveFileProtocol(param);
2367 result = alignFrame.parseFeaturesFile(param, protocol);
2370 param = applet.getParameter("showFeatureSettings");
2371 if (param != null && param.equalsIgnoreCase(TRUE))
2373 alignFrame.viewport.setShowSequenceFeatures(true);
2374 new FeatureSettings(alignFrame.alignPanel);
2380 * Load a score file if specified by parameter. Returns true if file was
2381 * loaded, else false.
2385 protected boolean loadScoreFile(AlignFrame alignFrame)
2387 boolean result = false;
2388 String sScoreFile = applet.getParameter("scoreFile");
2389 if (sScoreFile != null && !"".equals(sScoreFile))
2396 "Attempting to load T-COFFEE score file from the scoreFile parameter");
2398 result = alignFrame.loadScoreFile(sScoreFile);
2402 "Failed to parse T-COFFEE parameter as a valid score file ('"
2403 + sScoreFile + "')");
2405 } catch (Exception e)
2407 System.err.printf("Cannot read score file: '%s'. Cause: %s \n",
2408 sScoreFile, e.getMessage());
2415 * Load a tree for the alignment if specified by parameter. Returns true if
2416 * a tree was loaded, else false.
2421 protected boolean loadTree(AlignFrame alignFrame)
2423 boolean result = false;
2424 String treeFile = applet.getParameter("tree");
2425 if (treeFile == null)
2427 treeFile = applet.getParameter("treeFile");
2430 if (treeFile != null)
2434 treeFile = resolveFileProtocol(treeFile);
2435 NewickFile fin = new NewickFile(treeFile, protocol);
2438 if (fin.getTree() != null)
2440 alignFrame.loadTree(fin, treeFile);
2442 dbgMsg("Successfully imported tree.");
2446 dbgMsg("Tree parameter did not resolve to a valid tree.");
2448 } catch (Exception ex)
2450 ex.printStackTrace();
2457 * Discovers whether the given file is in the Applet Archive
2463 boolean inArchive(String f)
2465 // This might throw a security exception in certain browsers
2466 // Netscape Communicator for instance.
2469 boolean rtn = (getClass().getResourceAsStream("/" + f) != null);
2472 System.err.println("Resource '" + f + "' was "
2473 + (rtn ? "" : "not ") + "located by classloader.");
2476 } catch (Exception ex)
2478 System.out.println("Exception checking resources: " + f + " " + ex);
2485 * @return the default alignFrame acted on by the public applet methods. May
2486 * return null with an error message on System.err indicating the
2489 public AlignFrame getDefaultTargetFrame()
2491 if (currentAlignFrame != null)
2493 return currentAlignFrame;
2495 if (initialAlignFrame != null)
2497 return initialAlignFrame;
2500 "Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
2505 * separator used for separatorList
2507 protected String separator = "" + ((char) 0x00AC); // the default used to be
2508 // '|' but many sequence
2509 // IDS include pipes.
2512 * set to enable the URL based javascript execution mechanism
2514 public boolean jsfallbackEnabled = false;
2517 * parse the string into a list
2520 * @return elements separated by separator
2522 public String[] separatorListToArray(String list)
2524 return separatorListToArray(list, separator);
2528 * parse the string into a list
2532 * @return elements separated by separator
2534 public static String[] separatorListToArray(String list, String separator)
2536 // TODO use StringUtils version (slightly different...)
2537 int seplen = separator.length();
2538 if (list == null || list.equals("") || list.equals(separator))
2542 java.util.Vector jv = new Vector();
2544 while ((pos = list.indexOf(separator, cp)) > cp)
2546 jv.addElement(list.substring(cp, pos));
2549 if (cp < list.length())
2551 String c = list.substring(cp);
2552 if (!c.equals(separator))
2559 String[] v = new String[jv.size()];
2560 for (int i = 0; i < v.length; i++)
2562 v[i] = (String) jv.elementAt(i);
2564 jv.removeAllElements();
2567 System.err.println("Array from '" + separator
2568 + "' separated List:\n" + v.length);
2569 for (int i = 0; i < v.length; i++)
2571 System.err.println("item " + i + " '" + v[i] + "'");
2579 "Empty Array from '" + separator + "' separated List");
2585 * concatenate the list with separator
2588 * @return concatenated string
2590 public String arrayToSeparatorList(String[] list)
2592 return arrayToSeparatorList(list, separator);
2596 * concatenate the list with separator
2600 * @return concatenated string
2602 public static String arrayToSeparatorList(String[] list, String separator)
2604 // TODO use StringUtils version
2605 StringBuffer v = new StringBuffer();
2606 if (list != null && list.length > 0)
2608 for (int i = 0, iSize = list.length; i < iSize; i++)
2610 if (list[i] != null)
2614 v.append(separator);
2622 .println("Returning '" + separator + "' separated List:\n");
2623 System.err.println(v);
2625 return v.toString();
2630 "Returning empty '" + separator + "' separated List\n");
2632 return "" + separator;
2638 * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
2641 public String getFeatureGroups()
2643 String lst = arrayToSeparatorList(
2644 getDefaultTargetFrame().getFeatureGroups());
2652 * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame
2656 public String getFeatureGroupsOn(AlignFrame alf)
2658 String lst = arrayToSeparatorList(alf.getFeatureGroups());
2665 * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)
2668 public String getFeatureGroupsOfState(boolean visible)
2670 return arrayToSeparatorList(
2671 getDefaultTargetFrame().getFeatureGroupsOfState(visible));
2678 * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui
2679 * .AlignFrame, boolean)
2682 public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
2684 return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
2690 * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui.
2691 * AlignFrame, java.lang.String, boolean)
2694 public void setFeatureGroupStateOn(final AlignFrame alf,
2695 final String groups, boolean state)
2697 final boolean st = state;// !(state==null || state.equals("") ||
2698 // state.toLowerCase().equals("false"));
2699 java.awt.EventQueue.invokeLater(new Runnable()
2704 alf.setFeatureGroupState(separatorListToArray(groups), st);
2712 * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupState(java.lang.String,
2716 public void setFeatureGroupState(String groups, boolean state)
2718 setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
2724 * @see jalview.bin.JalviewLiteJsApi#getSeparator()
2727 public String getSeparator()
2735 * @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String)
2738 public void setSeparator(String separator)
2740 if (separator == null || separator.length() < 1)
2743 separator = "" + ((char) 0x00AC);
2745 this.separator = separator;
2748 System.err.println("Default Separator now: '" + separator + "'");
2753 * get boolean value of applet parameter 'name' and return default if
2754 * parameter is not set
2759 * the value to return otherwise
2760 * @return true or false
2762 public boolean getDefaultParameter(String name, boolean def)
2765 if ((stn = getParameter(name)) == null)
2769 if (TRUE.equalsIgnoreCase(stn))
2779 * @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame,
2780 * java.lang.String, java.lang.String, java.lang.String)
2783 public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
2784 String pdbEntryString, String pdbFile)
2786 return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);
2789 protected void setAlignPdbStructures(boolean alignPdbStructures)
2791 this.alignPdbStructures = alignPdbStructures;
2794 public boolean isAlignPdbStructures()
2796 return alignPdbStructures;
2802 // callInitCallback();
2805 private Hashtable<String, long[]> jshashes = new Hashtable<String, long[]>();
2807 private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<String, Hashtable<String, String[]>>();
2809 public void setJsMessageSet(String messageclass, String viewId,
2810 String[] colcommands)
2812 Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
2815 msgset = new Hashtable<String, String[]>();
2816 jsmessages.put(messageclass, msgset);
2818 msgset.put(viewId, colcommands);
2819 long[] l = new long[colcommands.length];
2820 for (int i = 0; i < colcommands.length; i++)
2822 l[i] = colcommands[i].hashCode();
2824 jshashes.put(messageclass + "|" + viewId, l);
2830 * @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String,
2834 public String getJsMessage(String messageclass, String viewId)
2836 Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
2839 String[] msgs = msgset.get(viewId);
2842 for (int i = 0; i < msgs.length; i++)
2844 if (msgs[i] != null)
2856 public boolean isJsMessageSetChanged(String string, String string2,
2857 String[] colcommands)
2859 long[] l = jshashes.get(string + "|" + string2);
2860 if (l == null && colcommands != null)
2864 for (int i = 0; i < colcommands.length; i++)
2866 if (l[i] != colcommands[i].hashCode())
2874 private Vector jsExecQueue = new Vector();
2876 public Vector getJsExecQueue()
2881 public void setExecutor(JSFunctionExec jsFunctionExec2)
2883 jsFunctionExec = jsFunctionExec2;
2887 * return the given colour value parameter or the given default if parameter
2894 public Color getDefaultColourParameter(String colparam, Color defcolour)
2896 String colprop = getParameter(colparam);
2897 if (colprop == null || colprop.trim().length() == 0)
2901 Color col = ColorUtils.parseColourString(colprop);
2904 System.err.println("Couldn't parse '" + colprop + "' as a colour for "
2907 return (col == null) ? defcolour : col;
2910 public void openJalviewHelpUrl()
2912 String helpUrl = getParameter("jalviewhelpurl");
2913 if (helpUrl == null || helpUrl.trim().length() < 5)
2915 helpUrl = "http://www.jalview.org/help.html";
2917 showURL(helpUrl, "HELP");
2921 * form a complete URL given a path to a resource and a reference location on
2925 * - an absolute path on the same server as localref or a document
2926 * located relative to localref
2928 * - a URL on the same server as url
2929 * @return a complete URL for the resource located by url
2931 private String resolveUrlForLocalOrAbsolute(String targetPath,
2934 String resolvedPath = "";
2935 if (targetPath.startsWith("/"))
2937 String codebase = localref.toString();
2938 String localfile = localref.getFile();
2939 resolvedPath = codebase.substring(0,
2940 codebase.length() - localfile.length()) + targetPath;
2941 return resolvedPath;
2945 * get URL path and strip off any trailing file e.g.
2946 * www.jalview.org/examples/index.html#applets?a=b is trimmed to
2947 * www.jalview.org/examples/
2949 String urlPath = localref.toString();
2950 String directoryPath = urlPath;
2951 int lastSeparator = directoryPath.lastIndexOf("/");
2952 if (lastSeparator > 0)
2954 directoryPath = directoryPath.substring(0, lastSeparator + 1);
2957 if (targetPath.startsWith("/"))
2960 * construct absolute URL to a file on the server - this is not allowed?
2962 // String localfile = localref.getFile();
2963 // resolvedPath = urlPath.substring(0,
2964 // urlPath.length() - localfile.length())
2966 resolvedPath = directoryPath + targetPath.substring(1);
2970 resolvedPath = directoryPath + targetPath;
2975 "resolveUrlForLocalOrAbsolute returning " + resolvedPath);
2977 return resolvedPath;
2981 * open a URL in the browser - resolving it according to relative refs and
2982 * coping with javascript: protocol if necessary.
2987 public void showURL(String url, String target)
2991 if (url.indexOf(":") == -1)
2993 // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
2995 // Should really use docbase, not codebase.
2997 url = resolveUrlForLocalOrAbsolute(url,
2998 prepend = getDefaultParameter("resolvetocodebase", false)
3000 : getDocumentBase());
3003 System.err.println("Show url (prepended " + prepend
3004 + " - toggle resolvetocodebase if code/docbase resolution is wrong): "
3012 System.err.println("Show url: " + url);
3015 if (url.indexOf("javascript:") == 0)
3017 // no target for the javascript context
3018 getAppletContext().showDocument(new java.net.URL(url));
3022 getAppletContext().showDocument(new java.net.URL(url), target);
3024 } catch (Exception ex)
3026 ex.printStackTrace();
3031 * bind structures in a viewer to any matching sequences in an alignFrame (use
3032 * sequenceIds to limit scope of search to specific sequences)
3036 * @param sequenceIds
3037 * @return TODO: consider making an exception structure for indicating when
3038 * binding fails public SequenceStructureBinding
3039 * addStructureViewInstance( AlignFrame alFrame, Object viewer, String
3042 * if (sequenceIds != null && sequenceIds.length() > 0) { return
3043 * alFrame.addStructureViewInstance(viewer,
3044 * separatorListToArray(sequenceIds)); } else { return
3045 * alFrame.addStructureViewInstance(viewer, null); } // return null; }