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Coverage Report

  1. Project Clover database Wed Dec 3 2025 17:03:17 GMT
  2. Package jalview.bin

File JalviewJSApp.java

 

Coverage histogram

../../img/srcFileCovDistChart0.png
60% of files have more coverage

Code metrics

288
519
55
2
1,691
1,212
242
0.47
9.44
27.5
4.4

Classes

Class Line # Actions
JalviewJSApp 55 490 222
0.00%
JalviewJSApp.JsSelectionListener 74 29 20
0.00%
 

Contributing tests

No tests hitting this source file were found.

Source view

1    package jalview.bin;
2   
3    import java.awt.EventQueue;
4    //import java.applet.AppletContext;
5    import java.io.IOException;
6    import java.net.URL;
7    import java.util.ArrayList;
8    import java.util.List;
9    import java.util.StringTokenizer;
10    import java.util.Vector;
11   
12    import javax.swing.SwingUtilities;
13   
14    import jalview.api.JalviewJSApi;
15    import jalview.api.StructureSelectionManagerProvider;
16    import jalview.datamodel.Alignment;
17    import jalview.datamodel.AlignmentI;
18    import jalview.datamodel.AlignmentOrder;
19    import jalview.datamodel.ColumnSelection;
20    import jalview.datamodel.HiddenColumns;
21    import jalview.datamodel.PDBEntry;
22    import jalview.datamodel.Sequence;
23    import jalview.datamodel.SequenceGroup;
24    import jalview.datamodel.SequenceI;
25    import jalview.gui.AlignFrame;
26    import jalview.gui.AlignViewport;
27    import jalview.gui.CalculationChooser;
28    import jalview.gui.Desktop;
29    import jalview.gui.StructureViewer;
30    import jalview.io.AnnotationFile;
31    import jalview.io.AppletFormatAdapter;
32    import jalview.io.DataSourceType;
33    import jalview.io.FeaturesFile;
34    import jalview.io.FileFormat;
35    import jalview.io.FileFormatI;
36    import jalview.io.FileFormats;
37    import jalview.io.IdentifyFile;
38    import jalview.io.JPredFile;
39    import jalview.io.JnetAnnotationMaker;
40    import jalview.io.NewickFile;
41    import jalview.structure.SelectionListener;
42    import jalview.structure.SelectionSource;
43    import jalview.structure.StructureSelectionManager;
44    import jalview.util.HttpUtils;
45    import jalview.util.Platform;
46   
47    /**
48    * Basically the JalviewLite application, but without JalviewLite
49    *
50    * Processing all "applet parameters" and also all "applet interface" methods.
51    *
52    * @author hansonr
53    *
54    */
 
55    public class JalviewJSApp implements JalviewJSApi
56    {
57    private ArgsParser aparser;
58   
59    private String[] ret = new String[1];
60   
61    // private boolean alignPDBStructures; From JalviewLite; not implemented
62   
63    private String separator = "\u00AC"; // JalviewLite note: the default used to
64    // be '|', but many sequence IDS include
65    // pipes.
66   
67    /**
68    * We maintain a pointer to the jalview instance here, because only with that
69    * do we have a direct connection from the JavaScript "applet" object to the
70    * proper instance of Jalview in case there are multiple applets on a page.
71    */
72    private Jalview jalview;
73   
 
74    public class JsSelectionListener
75    implements jalview.structure.SelectionListener
76    {
77   
78    AlignFrame _alf;
79   
80    String _listener;
81   
 
82  0 toggle public JsSelectionListener(AlignFrame alf, String listener)
83    {
84  0 _alf = alf;
85  0 _listener = listener;
86    }
87   
 
88  0 toggle public boolean isFor(AlignFrame alf, String listener)
89    {
90  0 return (_alf == null || _alf == alf) && _listener.equals(listener);
91    }
92   
 
93  0 toggle @Override
94    public void selection(SequenceGroup seqsel, ColumnSelection colsel,
95    HiddenColumns hidden, SelectionSource source)
96    {
97    // System.err.println("Testing selection event relay to
98    // jsfunction:"+_listener);
99  0 String setid = "";
100  0 AlignFrame srcFrame = (_alf == null ? getCurrentAlignFrame() : _alf);
101  0 if (source != null)
102    {
103  0 if (source instanceof AlignViewport
104    && srcFrame.getViewport() != source)
105    {
106  0 return;
107    }
108    }
109  0 String[] seqs = new String[] {};
110  0 String[] cols = new String[] {};
111  0 int strt = 0, end = (srcFrame == null) ? -1
112    : srcFrame.alignPanel.av.getAlignment().getWidth();
113  0 if (seqsel != null && seqsel.getSize() > 0)
114    {
115  0 seqs = new String[seqsel.getSize()];
116  0 for (int i = 0; i < seqs.length; i++)
117    {
118  0 seqs[i] = seqsel.getSequenceAt(i).getName();
119    }
120  0 if (strt < seqsel.getStartRes())
121    {
122  0 strt = seqsel.getStartRes();
123    }
124  0 if (end == -1 || end > seqsel.getEndRes())
125    {
126  0 end = seqsel.getEndRes();
127    }
128    }
129  0 if (colsel != null && !colsel.isEmpty())
130    {
131  0 if (end == -1)
132    {
133  0 end = colsel.getMax() + 1;
134    }
135  0 cols = new String[colsel.getSelected().size()];
136  0 for (int i = 0; i < cols.length; i++)
137    {
138  0 cols[i] = "" + (1 + colsel.getSelected().get(i).intValue());
139    }
140    }
141    else
142    {
143  0 if (seqsel != null && seqsel.getSize() > 0)
144    {
145    // send a valid range, otherwise we send the empty selection
146  0 cols = new String[1];
147  0 cols[0] = "" + (1 + strt) + "-" + (1 + end);
148    }
149    }
150  0 doSendCallback(_listener,
151    new Object[]
152    { Jalview.getInstance().j2sAppletID, srcFrame, source, setid,
153    seqs, cols });
154    }
155   
156    }
157   
 
158  0 toggle public JalviewJSApp(Jalview jalview, ArgsParser aparser)
159    {
160  0 Platform.setAppClass(this);
161  0 this.jalview = jalview;
162  0 this.aparser = aparser;
163    }
164   
 
165  0 toggle @Override
166    public boolean addPdbFile(String sequenceId, String pdbId, String pdbFile,
167    AlignFrame alf)
168    {
169  0 if (alf == null)
170    {
171  0 alf = getCurrentAlignFrame();
172    }
173  0 SequenceI seq = alf.getViewport().getAlignment().findName(sequenceId);
174  0 if (seq != null)
175    {
176  0 Vector<PDBEntry> pdbe = seq.getAllPDBEntries();
177  0 PDBEntry pdbentry = null;
178  0 if (pdbe != null && pdbe.size() > 0)
179    {
180  0 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
181    {
182  0 pdbentry = pdbe.elementAt(pe);
183  0 if (!pdbentry.getId().equals(pdbId)
184    || pdbFile != null && !pdbentry.getFile().equals(pdbFile))
185    {
186  0 pdbentry = null;
187    }
188    }
189    }
190  0 if (pdbentry == null)
191    {
192  0 pdbentry = new PDBEntry(pdbId, null, pdbFile);
193  0 if (pdbFile != null)
194    {
195  0 DataSourceType protocol = AppletFormatAdapter
196    .resolveProtocol(pdbFile, FileFormat.PDB);
197  0 if (protocol == null)
198  0 return false;
199  0 pdbentry.setProperty("protocol", protocol);
200    }
201  0 seq.addPDBId(pdbentry);
202  0 alf.alignPanel.getStructureSelectionManager()
203    .registerPDBEntry(pdbentry);
204    }
205    }
206  0 return true;
207    }
208   
 
209  0 toggle @Override
210    public String getAlignment(String format, boolean addSuffix,
211    AlignFrame alf)
212    {
213  0 try
214    {
215  0 if (alf == null)
216    {
217  0 alf = getCurrentAlignFrame();
218    }
219   
220  0 FileFormatI theFormat = FileFormats.getInstance().forName(format);
221  0 String reply = new AppletFormatAdapter().formatSequences(theFormat,
222    alf.getViewport().getAlignment(), addSuffix);
223  0 return reply;
224    } catch (IllegalArgumentException ex)
225    {
226  0 ex.printStackTrace();
227  0 return "Error retrieving alignment, possibly invalid format specifier: "
228    + format;
229    }
230    }
231   
 
232  0 toggle @Override
233    public String[] getAlignmentOrder(AlignFrame alf)
234    {
235  0 if (alf == null)
236    {
237  0 alf = getCurrentAlignFrame();
238    }
239  0 AlignmentI alorder = alf.getViewport().getAlignment();
240  0 String[] order = new String[alorder.getHeight()];
241  0 for (int i = 0; i < order.length; i++)
242    {
243  0 order[i] = alorder.getSequenceAt(i).getName();
244    }
245  0 return order;// arrayToSeparatorList(order, sep);
246    }
247   
 
248  0 toggle @Override
249    public String getAnnotation(AlignFrame alf)
250    {
251  0 if (alf == null)
252    {
253  0 alf = getCurrentAlignFrame();
254    }
255  0 String annotation = new AnnotationFile()
256    .printAnnotationsForView(alf.getViewport());
257  0 return annotation;
258    }
259   
260    /**
261    * Get the applet-like code base even though this is an application.
262    */
263   
 
264  0 toggle @Override
265    public URL getCodeBase()
266    {
267  0 return Platform.getCodeBase();
268    }
269   
 
270  0 toggle @Override
271    public AlignFrame getCurrentAlignFrame()
272    {
273    // if (jalview != Jalview.getInstance() || jalview.currentAlignFrame !=
274    // Jalview.getCurrentAlignFrame()) {
275    // /** @j2sNative debugger */
276    // }
277  0 return jalview.currentAlignFrame;
278    }
279   
280    /**
281    * Get the applet-like document base even though this is an application.
282    */
283   
 
284  0 toggle @Override
285    public URL getDocumentBase()
286    {
287  0 return Platform.getDocumentBase();
288    }
289   
 
290  0 toggle @Override
291    public String[] getFeatureGroups(AlignFrame alf)
292    {
293  0 if (alf == null)
294    {
295  0 alf = getCurrentAlignFrame();
296    }
297  0 return alf.getFeatureGroups();
298    }
299   
 
300  0 toggle @Override
301    public String[] getFeatureGroupsOfState(boolean visible, AlignFrame alf)
302    {
303  0 if (alf == null)
304    {
305  0 alf = getCurrentAlignFrame();
306    }
307  0 return alf.getFeatureGroupsOfState(visible);
308    }
309   
310    /**
311    * JavaScript interface to print the alignment frame
312    *
313    * @param format
314    * "jalview" or "gff" with or without ";includeComplement" or
315    * ";includeNonpositional"; default with no ";" is
316    * ";includeNonpositional"
317    * @param alf
318    *
319    * @return
320    */
 
321  0 toggle @Override
322    public String getFeatures(String format, AlignFrame alf)
323    {
324  0 if (alf == null)
325    {
326  0 alf = getCurrentAlignFrame();
327    }
328  0 String features;
329  0 FeaturesFile formatter = new FeaturesFile();
330  0 format = format.toLowerCase();
331  0 if (format.indexOf(";") < 0)
332  0 format += ";includenonpositional";
333  0 boolean nonpos = format.indexOf(";includenonpositional") >= 0;
334  0 boolean compl = format.indexOf(";includecomplement") >= 0;
335  0 if (format.startsWith("jalview"))
336    {
337  0 features = formatter.printJalviewFormat(
338    alf.getViewport().getAlignment().getSequencesArray(),
339    alf.alignPanel.getFeatureRenderer(), nonpos, compl);
340    }
341    else
342    {
343  0 features = formatter.printGffFormat(
344    alf.getViewport().getAlignment().getSequencesArray(),
345    alf.alignPanel.getFeatureRenderer(), nonpos, compl);
346    }
347   
348  0 if (features == null)
349    {
350  0 features = "";
351    }
352  0 return features;
353   
354    }
355   
356    /**
357    * Get an applet parameter as a string.
358    *
359    */
 
360  0 toggle @Override
361    public String getParameter(String name)
362    {
363  0 return (String) aparser.getAppletValue(name, null, true);
364    }
365   
366    /**
367    * Get an applet parameter as an Object.
368    */
369   
 
370  0 toggle @Override
371    public Object getParameterAsObject(String name)
372    {
373  0 return aparser.getAppletValue(name, null, false);
374    }
375   
376    /**
377    * read sequence1...sequenceN as a raw alignment
378    *
379    * @param jalviewApp
380    * @return
381    */
 
382  0 toggle public String getPastedSequence(JalviewJSApp jalviewApp)
383    {
384  0 StringBuffer data = new StringBuffer("PASTE");
385  0 int i = 1;
386  0 String file = null;
387  0 while ((file = getParameter("sequence" + i)) != null)
388    {
389  0 data.append(file.toString() + "\n");
390  0 i++;
391    }
392  0 if (data.length() > 5)
393    {
394  0 file = data.toString();
395    }
396  0 return file;
397    }
398   
399    /**
400    * @j2sAlias getSelectedSequences
401    *
402    * @see jalview.appletgui.js.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
403    * .AlignFrame)
404    */
 
405  0 toggle @Override
406    public SequenceI[] getSelectedSequences(AlignFrame alf)
407    {
408    // return getSelectedSequencesFrom(alf, null);
409    // }
410    //
411    // @Override
412    // public SequenceI[] getSelectedSequencesFrom(AlignFrame alf, String sep)
413    // {
414  0 if (alf == null)
415    {
416  0 alf = getCurrentAlignFrame();
417    }
418  0 AlignViewport v = alf.getViewport();
419  0 if (v.getSelectionGroup() != null)
420    {
421  0 return v.getSelectionGroup().getSequencesInOrder(v.getAlignment());
422    }
423  0 return null;
424    }
425    // /**
426    // *
427    // * @see
428    // jalview.appletgui.js.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
429    // * .AlignFrame, java.lang.String)
430    // */
431    // @Override
432    // public void highlight(String sequenceId, String position,
433    // String alignedPosition)
434    // {
435    // highlightIn(null, sequenceId, position, alignedPosition);
436    // }
437   
438    /**
439    * @j2sAlias getSelectedSequencesAsAlignment
440    */
 
441  0 toggle @Override
442    public String getSelectedSequencesAsAlignment(String format,
443    boolean addSuffix, AlignFrame alf)
444    {
445   
446  0 if (alf == null)
447    {
448  0 alf = getCurrentAlignFrame();
449    }
450  0 try
451    {
452  0 AlignViewport vp = alf.getViewport();
453  0 FileFormatI theFormat = FileFormats.getInstance().forName(format);
454  0 if (vp.getSelectionGroup() != null)
455    {
456    // JBPNote: getSelectionAsNewSequence behaviour has changed - this
457    // method now returns a full copy of sequence data
458    // TODO consider using getSequenceSelection instead here
459  0 String reply = new AppletFormatAdapter().formatSequences(theFormat,
460    new Alignment(vp.getSelectionAsNewSequence()), addSuffix);
461  0 return reply;
462    }
463    } catch (IllegalArgumentException ex)
464    {
465  0 ex.printStackTrace();
466  0 return "Error retrieving alignment, possibly invalid format specifier: "
467    + format;
468    }
469  0 return "";
470    }
471   
 
472  0 toggle @Override
473    public void highlight(String sequenceId, String position,
474    String alignedPosition, AlignFrame alf)
475    {
476  0 if (alf == null)
477    {
478  0 alf = getCurrentAlignFrame();
479    }
480    // TODO: could try to highlight in all alignments if alf==null
481  0 jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
482    alf.getViewport().getAlignment().getSequencesArray());
483  0 final SequenceI sq = matcher.findIdMatch(sequenceId);
484  0 if (sq != null)
485    {
486  0 int apos = -1;
487  0 try
488    {
489  0 apos = Integer.valueOf(position).intValue();
490  0 apos--;
491    } catch (NumberFormatException ex)
492    {
493  0 return;
494    }
495  0 final int pos = apos;
496    // use vamsas listener to broadcast to all listeners in scope
497  0 if (alignedPosition != null && (alignedPosition.trim().length() == 0
498    || alignedPosition.toLowerCase().indexOf("false") > -1))
499    {
500  0 java.awt.EventQueue.invokeLater(new Runnable()
501    {
 
502  0 toggle @Override
503    public void run()
504    {
505  0 StructureSelectionManager
506    .getStructureSelectionManager(Desktop.getInstance())
507    .mouseOverVamsasSequence(sq, sq.findIndex(pos), null);
508    }
509    });
510    }
511    else
512    {
513  0 java.awt.EventQueue.invokeLater(new Runnable()
514    {
 
515  0 toggle @Override
516    public void run()
517    {
518  0 StructureSelectionManager
519    .getStructureSelectionManager(Desktop.getInstance())
520    .mouseOverVamsasSequence(sq, pos, null);
521    }
522    });
523    }
524    }
525    }
526   
 
527  0 toggle @Override
528    public AlignFrame loadAlignment(String text, String title, int width,
529    int height)
530    {
531  0 AlignmentI al = null;
532   
533  0 try
534    {
535  0 FileFormatI format = new IdentifyFile().identify(text,
536    DataSourceType.PASTE);
537  0 al = new AppletFormatAdapter().readFile(text, DataSourceType.PASTE,
538    format);
539  0 if (al.getHeight() > 0)
540    {
541  0 return new AlignFrame(al,
542  0 width > 0 ? width : AlignFrame.DEFAULT_WIDTH,
543  0 height > 0 ? height : AlignFrame.DEFAULT_HEIGHT, title);
544    }
545    } catch (IOException ex)
546    {
547  0 ex.printStackTrace();
548    }
549  0 return null;
550    }
551   
 
552  0 toggle @Override
553    public void loadAnnotation(String annotation, AlignFrame alf)
554    {
555  0 if (alf == null)
556    {
557  0 alf = getCurrentAlignFrame();
558    }
559  0 if (new AnnotationFile().annotateAlignmentView(alf.getViewport(),
560    annotation, DataSourceType.PASTE))
561    {
562  0 alf.alignPanel.fontChanged();
563  0 alf.alignPanel.setScrollValues(0, 0);
564    }
565    else
566    {
567  0 alf.parseFeaturesFile(annotation, DataSourceType.PASTE);
568    }
569    }
570   
 
571  0 toggle @Override
572    public boolean loadFeatures(String features, boolean autoenabledisplay,
573    AlignFrame alf)
574    {
575  0 if (alf == null)
576    {
577  0 alf = getCurrentAlignFrame();
578    }
579  0 boolean ret = alf.parseFeaturesFile(features, DataSourceType.PASTE);
580  0 if (!ret)
581    {
582  0 return false;
583    }
584  0 if (autoenabledisplay)
585    {
586  0 alf.getViewport().setShowSequenceFeatures(true);
587    // this next was for a checkbox in JalviewLite
588    // ((AlignFrame) alf).getViewport().sequenceFeatures.setState(true);
589    }
590  0 return true;
591    }
592   
 
593  0 toggle @Override
594    public boolean loadScoreFile(String fileName, AlignFrame alf)
595    {
596  0 try
597    {
598  0 (alf == null ? getCurrentAlignFrame() : alf)
599    .loadJalviewDataFile(fileName, null, null, null);
600  0 return true;
601    } catch (Throwable t)
602    {
603  0 return false;
604    }
605    }
606   
607    /**
608    * @j2sAlias openPcaPanel
609    *
610    * public static method for JalviewJS API to open a PCAPanel without
611    * necessarily using a dialog.
612    * @param modelName
613    * @param alf
614    *
615    * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences"
616    * if number of sequences selected is inappropriate
617    */
 
618  0 toggle @Override
619    public Object openPcaPanel(String modelName, AlignFrame alf)
620    {
621  0 if (alf == null)
622    {
623  0 alf = getCurrentAlignFrame();
624    }
625  0 return CalculationChooser.openPcaPanel(alf, modelName, null);
626    }
627   
628    /**
629    * @j2sAlias openTreePanel
630    *
631    * Open a new Tree panel on the desktop statically. Params are
632    * standard (not set by Groovy). No dialog is opened.
633    * @param treeType
634    * @param modelName
635    * @param alf
636    *
637    * @return null, or the string "label.you_need_at_least_n_sequences" if number
638    * of sequences selected is inappropriate
639    */
 
640  0 toggle @Override
641    public Object openTreePanel(String treeType, String modelName,
642    AlignFrame alf)
643    {
644  0 if (alf == null)
645    {
646  0 alf = getCurrentAlignFrame();
647    }
648  0 return CalculationChooser.openTreePanel(alf, treeType, modelName, null);
649    }
650   
 
651  0 toggle @Override
652    public boolean orderAlignment(String[] ids, String undoName,
653    AlignFrame alf)
654    {
655  0 if (alf == null)
656  0 alf = getCurrentAlignFrame();
657  0 SequenceI[] sqs = null;
658  0 if (ids != null && ids.length > 0)
659    {
660  0 jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
661    alf.getViewport().getAlignment().getSequencesArray());
662  0 int s = 0;
663  0 sqs = new SequenceI[ids.length];
664  0 for (int i = 0; i < ids.length; i++)
665    {
666  0 if (ids[i].trim().length() == 0)
667    {
668  0 continue;
669    }
670  0 SequenceI sq = matcher.findIdMatch(ids[i]);
671  0 if (sq != null)
672    {
673  0 sqs[s++] = sq;
674    }
675    }
676  0 if (s > 0)
677    {
678  0 SequenceI[] sqq = new SequenceI[s];
679  0 System.arraycopy(sqs, 0, sqq, 0, s);
680  0 sqs = sqq;
681    }
682    else
683    {
684  0 sqs = null;
685    }
686    }
687  0 if (sqs == null)
688    {
689  0 return false;
690    }
691  0 ;
692  0 final AlignmentOrder aorder = new AlignmentOrder(sqs);
693   
694  0 if (undoName != null && undoName.trim().length() == 0)
695    {
696  0 undoName = null;
697    }
698  0 final String _undoName = undoName;
699    // TODO: deal with synchronization here: cannot raise any events until
700    // alfter
701    // this has returned.
702  0 return alf.sortBy(aorder, _undoName);
703    }
704   
705    /**
706    * Allow an outside entity to initiate the second half of argument parsing
707    * (only).
708    *
709    * @param args
710    * @return null is good
711    */
 
712  0 toggle @Override
713    public Object parseArguments(String[] args)
714    {
715   
716  0 try
717    {
718  0 jalview.parseArguments(new ArgsParser(args), false);
719  0 return null;
720    } catch (Throwable t)
721    {
722  0 return t;
723    }
724    }
725   
726    /**
727    * @j2sAlias parseFeatureFile
728    *
729    * @param filename
730    * @param alf
731    * @return
732    */
 
733  0 toggle @Override
734    public boolean parseFeaturesFile(String filename, AlignFrame alf)
735    {
736  0 ret[0] = filename;
737  0 DataSourceType protocol = resolveFileProtocol(ret);
738  0 if (protocol == null)
739  0 return false;
740  0 return (alf == null ? getCurrentAlignFrame() : alf)
741    .parseFeaturesFile(ret[0], protocol);
742    }
743   
 
744  0 toggle @Override
745    public void removeSelectionListener(String listener, AlignFrame alf)
746    {
747   
748  0 List<SelectionListener> listeners = Desktop
749    .getStructureSelectionManager().getListeners();
750  0 for (int i = listeners.size(); --i >= 0;)
751    {
752  0 SelectionListener l = listeners.get(i);
753  0 if (l instanceof JsSelectionListener
754    && ((JsSelectionListener) l).isFor(alf, listener))
755    {
756  0 listeners.remove(i);
757  0 break;
758    }
759    }
760    }
761   
 
762  0 toggle private DataSourceType resolveFileProtocol(String[] retPath)
763    {
764  0 String path = retPath[0];
765    /*
766    * is it paste data?
767    */
768  0 if (path.startsWith("PASTE"))
769    {
770  0 retPath[0] = path.substring(5);
771  0 return DataSourceType.PASTE;
772    }
773   
774    /*
775    * is it a URL?
776    */
777  0 if (path.indexOf("://") >= 0)
778    {
779  0 return DataSourceType.URL;
780    }
781   
782    /*
783    * try relative to document root
784    */
785  0 URL documentBase = getDocumentBase();
786  0 String withDocBase = resolveUrlForLocalOrAbsolute(path, documentBase);
787  0 if (HttpUtils.isValidUrl(withDocBase))
788    {
789    // if (debug)
790    // {
791    // System.err.println("Prepended document base '" + documentBase
792    // + "' to make: '" + withDocBase + "'");
793    // }
794  0 retPath[0] = withDocBase;
795  0 return DataSourceType.URL;
796    }
797   
798    /*
799    * try relative to codebase (if different to document base)
800    */
801  0 URL codeBase = getCodeBase();
802  0 String withCodeBase = resolveUrlForLocalOrAbsolute(path, codeBase);
803  0 if (!withCodeBase.equals(withDocBase)
804    && HttpUtils.isValidUrl(withCodeBase))
805    {
806    // if (debug)
807    // {
808    // System.err.println("Prepended codebase '" + codeBase
809    // + "' to make: '" + withCodeBase + "'");
810    // }
811  0 retPath[0] = withCodeBase;
812  0 return DataSourceType.URL;
813    }
814   
815    /*
816    * try locating by classloader; try this last so files in the directory
817    * are resolved using document base
818    */
819  0 if (inArchive(getClass(), path))
820    {
821  0 return DataSourceType.CLASSLOADER;
822    }
823  0 return null;
824    }
825   
 
826  0 toggle @Override
827    public void scrollViewTo(int topRow, int leftHandColumn, AlignFrame alf)
828    {
829    // TODO test
830  0 java.awt.EventQueue.invokeLater(new Runnable()
831    {
 
832  0 toggle @Override
833    public void run()
834    {
835  0 try
836    {
837  0 (alf == null ? getCurrentAlignFrame() : alf).scrollTo(topRow,
838    leftHandColumn);
839    } catch (Exception ex)
840    {
841  0 System.err.println("Couldn't parse integer arguments (topRow='"
842    + topRow + "' and leftHandColumn='" + leftHandColumn
843    + "')");
844  0 ex.printStackTrace();
845    }
846    }
847    });
848    }
849   
 
850  0 toggle @Override
851    public void select(String ids[], String cols[], AlignFrame alf)
852    {
853  0 if (alf == null)
854  0 alf = getCurrentAlignFrame();
855  0 final SequenceGroup sel = new SequenceGroup();
856  0 final ColumnSelection csel = new ColumnSelection();
857  0 AlignmentI al = alf.getViewport().getAlignment();
858  0 jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
859    alf.getViewport().getAlignment().getSequencesArray());
860  0 int start = 0, end = al.getWidth(), alw = al.getWidth();
861  0 boolean seqsfound = true;
862  0 if (ids != null && ids.length > 0)
863    {
864  0 seqsfound = false;
865  0 for (int i = 0; i < ids.length; i++)
866    {
867  0 if (ids[i].trim().length() == 0)
868    {
869  0 continue;
870    }
871  0 SequenceI sq = matcher.findIdMatch(ids[i]);
872  0 if (sq != null)
873    {
874  0 seqsfound = true;
875  0 sel.addSequence(sq, false);
876    }
877    }
878    }
879  0 boolean inseqpos = false;
880  0 if (cols != null && cols.length > 0)
881    {
882  0 boolean seset = false;
883  0 for (int i = 0; i < cols.length; i++)
884    {
885  0 String cl = cols[i].trim();
886  0 if (cl.length() == 0)
887    {
888  0 continue;
889    }
890  0 int p;
891  0 if ((p = cl.indexOf("-")) > -1)
892    {
893  0 int from = -1, to = -1;
894  0 try
895    {
896  0 from = Integer.valueOf(cl.substring(0, p)).intValue();
897  0 from--;
898    } catch (NumberFormatException ex)
899    {
900  0 System.err.println(
901    "ERROR: Couldn't parse first integer in range element column selection string '"
902    + cl + "' - format is 'from-to'");
903  0 return;
904    }
905  0 try
906    {
907  0 to = Integer.valueOf(cl.substring(p + 1)).intValue();
908  0 to--;
909    } catch (NumberFormatException ex)
910    {
911  0 System.err.println(
912    "ERROR: Couldn't parse second integer in range element column selection string '"
913    + cl + "' - format is 'from-to'");
914  0 return;
915    }
916  0 if (from >= 0 && to >= 0)
917    {
918    // valid range
919  0 if (from < to)
920    {
921  0 int t = to;
922  0 to = from;
923  0 to = t;
924    }
925  0 if (!seset)
926    {
927  0 start = from;
928  0 end = to;
929  0 seset = true;
930    }
931    else
932    {
933    // comment to prevent range extension
934  0 if (start > from)
935    {
936  0 start = from;
937    }
938  0 if (end < to)
939    {
940  0 end = to;
941    }
942    }
943  0 for (int r = from; r <= to; r++)
944    {
945  0 if (r >= 0 && r < alw)
946    {
947  0 csel.addElement(r);
948    }
949    }
950    }
951    else
952    {
953  0 System.err.println("ERROR: Invalid Range '" + cl
954    + "' deparsed as [" + from + "," + to + "]");
955    }
956    }
957    else
958    {
959  0 int r = -1;
960  0 try
961    {
962  0 r = Integer.valueOf(cl).intValue();
963  0 r--;
964    } catch (NumberFormatException ex)
965    {
966  0 if (cl.toLowerCase().equals("sequence"))
967    {
968    // we are in the dataset sequence's coordinate frame.
969  0 inseqpos = true;
970    }
971    else
972    {
973  0 System.err.println(
974    "ERROR: Couldn't parse integer from point selection element of column selection string '"
975    + cl + "'");
976  0 return;
977    }
978    }
979  0 if (r >= 0 && r <= alw)
980    {
981  0 if (!seset)
982    {
983  0 start = r;
984  0 end = r;
985  0 seset = true;
986    }
987    else
988    {
989    // comment to prevent range extension
990  0 if (start > r)
991    {
992  0 start = r;
993    }
994  0 if (end < r)
995    {
996  0 end = r;
997    }
998    }
999  0 csel.addElement(r);
1000    }
1001    else
1002    {
1003  0 System.err.println("ERROR: Invalid Point selection '" + cl
1004    + "' deparsed as [" + r + "]");
1005    }
1006    }
1007    }
1008    }
1009  0 if (seqsfound)
1010    {
1011    // we only propagate the selection when it was the null selection, or the
1012    // given sequences were found in the alignment.
1013  0 if (inseqpos && sel.getSize() > 0)
1014    {
1015    // assume first sequence provides reference frame ?
1016  0 SequenceI rs = sel.getSequenceAt(0);
1017  0 start = rs.findIndex(start);
1018  0 end = rs.findIndex(end);
1019  0 List<Integer> cs = new ArrayList<>(csel.getSelected());
1020  0 csel.clear();
1021  0 for (Integer selectedCol : cs)
1022    {
1023  0 csel.addElement(rs.findIndex(selectedCol));
1024    }
1025    }
1026  0 sel.setStartRes(start);
1027  0 sel.setEndRes(end);
1028  0 AlignFrame af = alf;
1029  0 EventQueue.invokeLater(new Runnable()
1030    {
 
1031  0 toggle @Override
1032    public void run()
1033    {
1034  0 af.select(sel, csel,
1035    af.getCurrentView().getAlignment().getHiddenColumns());
1036    }
1037    });
1038    }
1039    }
1040   
1041    //
1042    // @Override
1043    // public void setFeatureGroupState(String[] groups, boolean state)
1044    // {
1045    // setFeatureGroupState(null, groups, state);
1046    // }
1047    //
1048    // @Override
1049    // public void setFeatureGroupState(String[] groups, boolean state)
1050    // { // JalviewLite API
1051    // setFeatureGroupStateOn(null, groups, state);
1052    // }
1053    //
 
1054  0 toggle @Override
1055    public void setFeatureGroupState(final String[] groups,
1056    boolean state, AlignFrame alf)
1057    {
1058    // setFeatureGroupState(alf, groups, state);
1059    // java.awt.EventQueue.invokeLater(new Runnable()
1060    // {
1061    // @Override
1062    // public void run()
1063    // {
1064    // (alf == null ? getCurrentAlignFrame() : alf)
1065    // .setFeatureGroupState(
1066    // separatorListToArray(groups, separator), state);
1067    // }
1068    // });
1069    // }
1070    //
1071    // public void setFeatureGroupState(AlignFrame alf, String[] groups, boolean
1072    // state) {
1073  0 (alf == null ? getCurrentAlignFrame() : alf)
1074    .setFeatureGroupState(groups, state);
1075    }
1076   
 
1077  0 toggle @Override
1078    public void setSelectionListener(String listener, AlignFrame alf)
1079    {
1080  0 Desktop.getStructureSelectionManager()
1081    .addSelectionListener(new JsSelectionListener(alf, listener));
1082    }
1083   
 
1084  0 toggle @Override
1085    public void showOverview()
1086    {
1087  0 getCurrentAlignFrame().overviewMenuItem_actionPerformed(null);
1088    }
1089   
1090    /**
1091    * @j2sAlias showStructure
1092    */
 
1093  0 toggle @Override
1094    public void showStructure(String pdbID, String fileType, AlignFrame alf)
1095    {
1096  0 if (alf == null)
1097  0 alf = getCurrentAlignFrame();
1098  0 PDBEntry pe = null;
1099  0 SequenceI[] seqs = null;
1100  0 if (pdbID == null)
1101    {
1102  0 seqs = alf.getViewport().getSequenceSelection();
1103  0 if (seqs.length == 0)
1104  0 seqs = alf.getViewport().getAlignment().getSequencesArray();
1105  0 for (int i = 0; i < seqs.length; i++)
1106    {
1107  0 Vector<PDBEntry> list = seqs[i].getAllPDBEntries();
1108  0 if (list.size() > 0)
1109    {
1110  0 pe = list.get(0);
1111  0 break;
1112    }
1113    }
1114    }
1115  0 if (pe == null)
1116    {
1117  0 if (pdbID == null)
1118  0 return;
1119  0 pe = new PDBEntry(pdbID, null, fileType);
1120  0 List<SequenceI> list = alf.getViewport().getAlignment()
1121    .getSequences();
1122  0 List<SequenceI> tmp = new ArrayList<SequenceI>();
1123  0 for (int i = 0; i < list.size(); i++)
1124    {
1125  0 SequenceI seq = list.get(i);
1126  0 if (seq.getPDBEntry(pdbID) != null)
1127    {
1128  0 tmp.add(seq);
1129    }
1130    }
1131  0 seqs = tmp.toArray(new SequenceI[tmp.size()]);
1132  0 alf.alignPanel.selectSequences(tmp);
1133    }
1134  0 StructureViewer.launchStructureViewer(alf.alignPanel, pe, seqs);
1135    }
1136   
1137    // private or package-private methods
1138   
1139    /**
1140    * form a complete URL given a path to a resource and a reference location on
1141    * the same server
1142    *
1143    * @param targetPath
1144    * - an absolute path on the same server as localref or a document
1145    * located relative to localref
1146    * @param localref
1147    * - a URL on the same server as url
1148    * @return a complete URL for the resource located by url
1149    */
 
1150  0 toggle private static String resolveUrlForLocalOrAbsolute(String targetPath,
1151    URL localref)
1152    {
1153  0 String resolvedPath = "";
1154  0 if (targetPath.startsWith("/"))
1155    {
1156  0 String codebase = localref.toString();
1157  0 String localfile = localref.getFile();
1158  0 resolvedPath = codebase.substring(0,
1159    codebase.length() - localfile.length()) + targetPath;
1160  0 return resolvedPath;
1161    }
1162   
1163    /*
1164    * get URL path and strip off any trailing file e.g.
1165    * www.jalview.org/examples/index.html#applets?a=b is trimmed to
1166    * www.jalview.org/examples/
1167    */
1168  0 String urlPath = localref.toString();
1169  0 String directoryPath = urlPath;
1170  0 int lastSeparator = directoryPath.lastIndexOf("/");
1171  0 if (lastSeparator > 0)
1172    {
1173  0 directoryPath = directoryPath.substring(0, lastSeparator + 1);
1174    }
1175   
1176  0 if (targetPath.startsWith("/"))
1177    {
1178    /*
1179    * construct absolute URL to a file on the server - this is not allowed?
1180    */
1181    // String localfile = localref.getFile();
1182    // resolvedPath = urlPath.substring(0,
1183    // urlPath.length() - localfile.length())
1184    // + targetPath;
1185  0 resolvedPath = directoryPath + targetPath.substring(1);
1186    }
1187    else
1188    {
1189  0 resolvedPath = directoryPath + targetPath;
1190    }
1191    // if (debug)
1192    // {
1193    // System.err.println(
1194    // "resolveUrlForLocalOrAbsolute returning " + resolvedPath);
1195    // }
1196  0 return resolvedPath;
1197    }
1198   
1199    /**
1200    * parse the string into a list
1201    *
1202    * @param list
1203    * @param separator
1204    * @return elements separated by separator
1205    */
 
1206  0 toggle private static String[] separatorListToArray(String list,
1207    String separator)
1208    {
1209    // TODO use StringUtils version (slightly different...)
1210  0 int seplen = separator.length();
1211  0 if (list == null || list.equals("") || list.equals(separator))
1212    {
1213  0 return null;
1214    }
1215  0 Vector<String> jv = new Vector<>();
1216  0 int cp = 0, pos;
1217  0 while ((pos = list.indexOf(separator, cp)) > cp)
1218    {
1219  0 jv.addElement(list.substring(cp, pos));
1220  0 cp = pos + seplen;
1221    }
1222  0 if (cp < list.length())
1223    {
1224  0 String c = list.substring(cp);
1225  0 if (!c.equals(separator))
1226    {
1227  0 jv.addElement(c);
1228    }
1229    }
1230  0 if (jv.size() > 0)
1231    {
1232  0 String[] v = new String[jv.size()];
1233  0 for (int i = 0; i < v.length; i++)
1234    {
1235  0 v[i] = jv.elementAt(i);
1236    }
1237  0 jv.removeAllElements();
1238  0 return v;
1239    }
1240  0 return null;
1241    }
1242   
1243    /**
1244    * Discovers whether the given file is in the Applet Archive
1245    *
1246    * @param f
1247    * String
1248    * @return boolean
1249    */
 
1250  0 toggle private static boolean inArchive(Class<?> c, String f)
1251    {
1252    // This might throw a security exception in certain browsers
1253    // Netscape Communicator for instance.
1254  0 try
1255    {
1256  0 boolean rtn = (c.getResourceAsStream("/" + f) != null);
1257  0 return rtn;
1258    } catch (Exception ex)
1259    {
1260  0 System.out.println("Exception checking resources: " + f + " " + ex);
1261  0 return false;
1262    }
1263    }
1264   
1265    /**
1266    * Allowing for a JavaScript function here.
1267    */
 
1268  0 toggle void callInitCallback()
1269    {
1270  0 Object initjscallback = getParameterAsObject("oninit");
1271  0 if (initjscallback != null)
1272    {
1273  0 SwingUtilities.invokeLater(new Runnable() {
1274   
 
1275  0 toggle @Override
1276    public void run()
1277    {
1278  0 try
1279    {
1280  0 doSendCallback(initjscallback, new Object[] {this});
1281    } catch (Exception e)
1282    {
1283  0 System.err.println("Exception when executing _oninit callback '"
1284    + initjscallback + "'.");
1285  0 e.printStackTrace();
1286    }
1287    }
1288   
1289    });
1290    }
1291    }
1292   
1293    /**
1294    * Pass the provided array prepended with Jalview.this
1295    *
1296    * Appropriated from org.jmol.appletjs.Jmol
1297    *
1298    * @param callback
1299    * a window function or "alert"
1300    * @param data
1301    * @return String return from the callback method.
1302    */
 
1303  0 toggle String doSendCallback(Object callback, Object[] data)
1304    {
1305  0 Jalview me = jalview;
1306   
1307  0 if (me != null && callback != null)
1308    {
1309    /**
1310    * @j2sNative
1311    *
1312    * try{
1313    *
1314    * if (callback == "alert") { alert(data[0]); return ""; } var
1315    * o; if (typeof callback == "function") { o = callback; } else
1316    * { if (!callback)return; var tokens = callback.split("."); o
1317    * = window[tokens[0]]; for (var i = 1; i < tokens.length; i++)
1318    * o = o[tokens[i]]; } var a = [me]; for (var i = 0; i <
1319    * data.length; i++) a.push(data[i] ? data[i].booleanValue &&
1320    * (data[i] = data[i].booleanValue()) : data[i]); return
1321    * o.apply(null,a) } catch (e) { System.out.println(callback +
1322    * " failed " + e); }
1323    */
1324    }
1325  0 return "";
1326    }
1327   
1328    /**
1329    * Initialize from Info.key/value pairs that match the old JalviewLite applet
1330    * parameters.
1331    *
1332    * See http://www.jalview.org/old/v2_8/examples/appletParameters.html
1333    *
1334    * Note that some of these parameters are handled as command-line arguments,
1335    * as determined in ArgsParser.
1336    *
1337    * @param alf
1338    */
 
1339  0 toggle void initFromParams(AlignFrame alf)
1340    {
1341  0 String sep = getParameter("separator");
1342  0 if (sep != null && sep.length() > 0)
1343    {
1344  0 separator = sep;
1345    }
1346  0 initTree(alf);
1347  0 initScoreFile(alf);
1348  0 initFeatures(alf);
1349  0 initAnnotations(alf);
1350  0 initJnetFile(alf);
1351  0 initPdbFiles(alf);
1352    }
1353   
1354    /**
1355    * Load annotations if specified by parameter. Returns true if loaded, else
1356    * false.
1357    *
1358    *
1359    * @param alignFrame
1360    * @return
1361    */
 
1362  0 toggle private boolean initAnnotations(AlignFrame alf)
1363    {
1364   
1365  0 String param = getParameter("annotations");
1366  0 if (param == null)
1367  0 return false;
1368  0 ret[0] = param;
1369  0 DataSourceType protocol = resolveFileProtocol(ret);
1370  0 param = ret[0];
1371  0 if (!new AnnotationFile().annotateAlignmentView(alf.getViewport(),
1372    param, protocol))
1373    {
1374  0 System.err.println("Annotations were not added from annotation file '"
1375    + param + "'");
1376  0 return false;
1377    }
1378  0 updateForAnnotations();
1379  0 return true;
1380    }
1381   
1382    /**
1383    * Load features file and view settings as specified by parameters. Returns
1384    * true if features were loaded, else false.
1385    *
1386    * @param
1387    *
1388    * @param alignFrame
1389    * @return
1390    */
 
1391  0 toggle private boolean initFeatures(AlignFrame alf)
1392    {
1393   
1394    // ///////////////////////////
1395    // modify display of features
1396    // we do this before any features have been loaded, ensuring any hidden
1397    // groups are hidden when features first displayed
1398    //
1399    // hide specific groups
1400    //
1401  0 String param = getParameter("hidefeaturegroups");
1402  0 if (param != null)
1403    {
1404  0 setFeatureGroupState(separatorListToArray(param, separator),
1405    false, alf);
1406    // setFeatureGroupStateOn(newAlignFrame, param, false);
1407    }
1408    // show specific groups
1409  0 param = getParameter("showfeaturegroups");
1410  0 if (param != null)
1411    {
1412  0 setFeatureGroupState(separatorListToArray(param, separator),
1413    true, alf);
1414    // setFeatureGroupStateOn(newAlignFrame, param, true);
1415    }
1416    // and now load features
1417  0 param = getParameter("features");
1418  0 if (param == null)
1419    {
1420  0 return false;
1421    }
1422  0 if (!parseFeaturesFile(param, alf))
1423  0 return false;
1424  0 param = getParameter("showFeatureSettings");
1425  0 if (param != null && param.equalsIgnoreCase("true"))
1426    {
1427  0 alf.showFeatureSettingsUI();
1428    }
1429  0 return true;
1430    }
1431   
1432    /**
1433    * Load in a Jnetfile if specified by parameter. Returns true if loaded, else
1434    * false.
1435    *
1436    * @param alignFrame
1437    * @return
1438    */
 
1439  0 toggle private boolean initJnetFile(AlignFrame alf)
1440    {
1441   
1442  0 String param = getParameter("jnetfile");
1443  0 if (param == null)
1444    {
1445    // jnet became jpred around 2016
1446  0 param = getParameter("jpredfile");
1447    }
1448  0 if (param != null)
1449    {
1450  0 try
1451    {
1452  0 ret[0] = param;
1453  0 DataSourceType protocol = resolveFileProtocol(ret);
1454  0 JPredFile predictions = new JPredFile(ret[0], protocol);
1455  0 JnetAnnotationMaker.add_annotation(predictions,
1456    alf.getViewport().getAlignment(), 0, false);
1457    // false == do not add sequence profile from concise output
1458  0 alf.getViewport().getAlignment().setupJPredAlignment();
1459  0 updateForAnnotations();
1460    } catch (Exception ex)
1461    {
1462  0 ex.printStackTrace();
1463  0 return false;
1464    }
1465    }
1466  0 return true;
1467    }
1468   
1469    /**
1470    * Load PDBFiles if any specified by parameter(s). Returns true if loaded,
1471    * else false.
1472    *
1473    * @param loaderFrame
1474    * @return
1475    */
 
1476  0 toggle private boolean initPdbFiles(AlignFrame alf)
1477    {
1478   
1479    /*
1480    * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6 -
1481    * related to JAL-434
1482    */
1483   
1484    // not supported (as for JalviewLite)
1485    // boolean doAlign = false;//"true".equalsIgnoreCase("" +
1486    // getAppletParameter("alignpdbfiles", false));
1487    // setAlignPdbStructures(doAlign);
1488    /*
1489    * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
1490    * PDB|1GAQ|1GAQ|C">
1491    *
1492    * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
1493    *
1494    * <param name="PDBfile3" value="1q0o Q45135_9MICO">
1495    */
1496   
1497    // Accumulate pdbs here if they are heading for the same view (if
1498    // alignPdbStructures is true)
1499    // ArrayList<Object[]> pdbs = new ArrayList<>();
1500    // init a lazy matcher if we're asked to
1501  0 boolean relaxed = "true"
1502    .equalsIgnoreCase(getParameter("relaxedidmatch"));
1503  0 jalview.analysis.SequenceIdMatcher matcher = relaxed
1504    ? new jalview.analysis.SequenceIdMatcher(
1505    alf.getViewport().getAlignment().getSequencesArray())
1506    : null;
1507   
1508  0 String param = getParameter("PDBFILE");
1509  0 int plast = (param == null ? 9 : 1);
1510  0 if (param == null && (param = getParameter("PDBFILE1")) == null)
1511    {
1512  0 return false;
1513    }
1514  0 for (int p = 1; p <= plast; p++)
1515    {
1516  0 if (p > 1)
1517    {
1518  0 param = getParameter("PDBFILE" + p);
1519  0 if (param == null)
1520  0 break;
1521    }
1522  0 PDBEntry pdb = new PDBEntry();
1523   
1524  0 String seqstring;
1525  0 SequenceI[] seqs = null;
1526  0 String[] chains = null;
1527   
1528  0 StringTokenizer st = new StringTokenizer(param, " ");
1529   
1530  0 if (st.countTokens() < 2)
1531    {
1532  0 String sequence = getParameter("PDBSEQ");
1533  0 if (sequence != null)
1534    {
1535  0 seqs = new SequenceI[] { matcher == null
1536    ? (Sequence) alf.getViewport().getAlignment()
1537    .findName(sequence)
1538    : matcher.findIdMatch(sequence) };
1539    }
1540   
1541    }
1542    else
1543    {
1544  0 param = st.nextToken();
1545  0 List<SequenceI> tmp = new ArrayList<>();
1546  0 List<String> tmp2 = new ArrayList<>();
1547   
1548  0 while (st.hasMoreTokens())
1549    {
1550  0 seqstring = st.nextToken();
1551  0 StringTokenizer st2 = new StringTokenizer(seqstring, "=");
1552  0 if (st2.countTokens() > 1)
1553    {
1554    // This is the chain
1555  0 tmp2.add(st2.nextToken());
1556  0 seqstring = st2.nextToken();
1557    }
1558  0 tmp.add(matcher == null
1559    ? (Sequence) alf.getViewport().getAlignment()
1560    .findName(seqstring)
1561    : matcher.findIdMatch(seqstring));
1562    }
1563   
1564  0 seqs = tmp.toArray(new SequenceI[tmp.size()]);
1565  0 if (tmp2.size() == tmp.size())
1566    {
1567  0 chains = tmp2.toArray(new String[tmp2.size()]);
1568    }
1569    }
1570  0 pdb.setId(param);
1571  0 ret[0] = param;
1572  0 DataSourceType protocol = resolveFileProtocol(ret);
1573    // TODO check JAL-357 for files in a jar (CLASSLOADER)
1574  0 pdb.setFile(ret[0]);
1575   
1576  0 if (seqs != null)
1577    {
1578  0 for (int i = 0; i < seqs.length; i++)
1579    {
1580  0 if (seqs[i] != null)
1581    {
1582  0 ((Sequence) seqs[i]).addPDBId(pdb);
1583  0 StructureSelectionManager
1584    .getStructureSelectionManager(
1585    (StructureSelectionManagerProvider) this)
1586    .registerPDBEntry(pdb);
1587    }
1588    }
1589   
1590    // if (doAlign)
1591    // {
1592    // pdbs.add(new Object[] { pdb, seqs, chains, protocol });
1593    // }
1594    // else
1595    {
1596  0 StructureViewer.launchStructureViewer(
1597  0 (alf == null ? getCurrentAlignFrame() : alf).alignPanel,
1598    pdb, seqs);
1599    }
1600    }
1601    }
1602    //
1603    // if (doAlign && pdbs.size() > 0)
1604    // {
1605    // SequenceI[][] seqs = new SequenceI[pdbs.size()][];
1606    // PDBEntry[] pdb = new PDBEntry[pdbs.size()];
1607    // String[][] chains = new String[pdbs.size()][];
1608    // String[] protocols = new String[pdbs.size()];
1609    // for (int pdbsi = 0, pdbsiSize = pdbs
1610    // .size(); pdbsi < pdbsiSize; pdbsi++)
1611    // {
1612    // Object[] o = pdbs.get(pdbsi);
1613    // pdb[pdbsi] = (PDBEntry) o[0];
1614    // seqs[pdbsi] = (SequenceI[]) o[1];
1615    // chains[pdbsi] = (String[]) o[2];
1616    // protocols[pdbsi] = (String) o[3];
1617    // }
1618    //// alignedStructureView(pdb, seqs, chains, protocols);
1619    // result = true;
1620    // }
1621  0 return true;
1622    }
1623   
1624    /**
1625    * Load a score file if specified by parameter. Returns true if file was
1626    * loaded, else false.
1627    *
1628    * @param loaderFrame
1629    */
 
1630  0 toggle private boolean initScoreFile(AlignFrame alf)
1631    {
1632   
1633  0 String sScoreFile = getParameter("scoreFile");
1634  0 if (sScoreFile != null && !"".equals(sScoreFile))
1635    {
1636  0 try
1637    {
1638  0 if (loadScoreFile(sScoreFile, alf))
1639    {
1640  0 return true;
1641    }
1642  0 System.err.println(
1643    "Failed to parse T-COFFEE parameter as a valid score file ('"
1644    + sScoreFile + "')");
1645    } catch (Exception e)
1646    {
1647  0 System.err.printf("Cannot read score file: '%s'. Cause: %s \n",
1648    sScoreFile, e.getMessage());
1649    }
1650    }
1651  0 return false;
1652    }
1653   
1654    /**
1655    * Load a tree for the alignment if specified by parameter. Returns true if a
1656    * tree was loaded, else false.
1657    *
1658    * @return
1659    */
 
1660  0 toggle private boolean initTree(AlignFrame alf)
1661    {
1662  0 String treeFile;
1663  0 if ((treeFile = getParameter("tree")) == null
1664    && (treeFile = getParameter("treefile")) == null)
1665  0 return false;
1666  0 if (alf == null)
1667  0 alf = getCurrentAlignFrame();
1668  0 try
1669    {
1670  0 ret[0] = treeFile;
1671  0 NewickFile nf = new NewickFile(treeFile, resolveFileProtocol(ret));
1672  0 nf.parse();
1673  0 if (nf.getTree() != null)
1674    {
1675  0 treeFile = ret[0];
1676  0 alf.getViewport()
1677    .setCurrentTree(alf.showNewickTree(nf, treeFile).getTree());
1678  0 return true;
1679    }
1680    } catch (Exception ex)
1681    {
1682  0 ex.printStackTrace();
1683    }
1684  0 return false;
1685    }
1686   
 
1687  0 toggle private void updateForAnnotations()
1688    {
1689  0 getCurrentAlignFrame().updateForAnnotations();
1690    }
1691    }
  • Report generated by OpenClover v 4.4.1 on Wed Dec 3 2025 17:13:21 GMT using coverage data from Wed Dec 3 2025 17:13:06 GMT.
  • OpenClover is free and open-source software.