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source: tags/ms_r18q1/DIST/DI_matr.cxx

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Last change on this file was 17110, checked in by westram, 6 years ago
reintegrates '' into 'trunk' implements #735 adds: log:branches/addtest@17040:17044 log:branches/tree@16921:17109
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1	// =============================================================== //
2	// //
3	// File : DI_matr.cxx //
4	// Purpose : //
5	// //
6	// Institute of Microbiology (Technical University Munich) //
7	// http://www.arb-home.de/ //
8	// //
9	// =============================================================== //
10
11	#include "di_protdist.hxx"
12	#include "di_clusters.hxx"
13	#include "dist.hxx"
14	#include "di_view_matrix.hxx"
15	#include "di_awars.hxx"
16
17	#include <neighbourjoin.hxx>
18	#include <AP_filter.hxx>
19	#include <CT_ctree.hxx>
20	#include <ColumnStat.hxx>
21
22	#include <awt.hxx>
23	#include <awt_sel_boxes.hxx>
24	#include <awt_filter.hxx>
25
26	#include <aw_preset.hxx>
27	#include <aw_awars.hxx>
28	#include <aw_file.hxx>
29	#include <aw_msg.hxx>
30	#include <aw_root.hxx>
31
32	#include <gui_aliview.hxx>
33
34	#include <climits>
35	#include <ctime>
36	#include <cmath>
37	#include <arb_sort.h>
38	#include <arb_global_defs.h>
39	#include <macros.hxx>
40	#include <ad_cb.h>
41	#include <awt_TreeAwars.hxx>
42	#include <arb_defs.h>
43
44	using std::string;
45
46	// --------------------------------------------------------------------------------
47
48	#define AWAR_DIST_BOOTSTRAP_COUNT AWAR_DIST_PREFIX "bootstrap/count"
49	#define AWAR_DIST_CANCEL_CHARS AWAR_DIST_PREFIX "cancel/chars"
50	#define AWAR_DIST_MATRIX_AUTO_RECALC AWAR_DIST_PREFIX "recalc"
51
52	#define AWAR_DIST_COLUMN_STAT_NAME AWAR_DIST_COLUMN_STAT_PREFIX "name"
53
54	#define AWAR_DIST_TREE_SORT_NAME "tmp/" AWAR_DIST_TREE_PREFIX "sort_tree_name"
55	#define AWAR_DIST_TREE_COMP_NAME "tmp/" AWAR_DIST_TREE_PREFIX "compr_tree_name"
56	#define AWAR_DIST_TREE_STD_NAME AWAR_DIST_TREE_PREFIX "tree_name"
57	#define AWAR_DIST_MATRIX_AUTO_CALC_TREE AWAR_DIST_TREE_PREFIX "autocalc"
58
59	#define AWAR_DIST_SAVE_MATRIX_TYPE AWAR_DIST_SAVE_MATRIX_BASE "/type"
60	#define AWAR_DIST_SAVE_MATRIX_FILENAME AWAR_DIST_SAVE_MATRIX_BASE "/file_name"
61
62	// --------------------------------------------------------------------------------
63
64	DI_GLOBAL_MATRIX GLOBAL_MATRIX;
65
66	static MatrixDisplay *matrixDisplay = NULp;
67	static AP_userdef_matrix userdef_DNA_matrix(AP_MAX, AWAR_DIST_MATRIX_DNA_BASE);
68
69	static AP_matrix *get_user_matrix() {
70	AW_root *awr = AW_root::SINGLETON;
71	if (!awr->awar(AWAR_DIST_MATRIX_DNA_ENABLED)->read_int()) {
72	return NULp;
73	}
74	userdef_DNA_matrix.update_from_awars(awr);
75	userdef_DNA_matrix.normize();
76	return &userdef_DNA_matrix;
77	}
78
79	class BoundWindowCallback : virtual Noncopyable {
80	AW_window *aww;
81	WindowCallback cb;
82	public:
83	BoundWindowCallback(AW_window *aww_, const WindowCallback& cb_)
84	: aww(aww_),
85	cb(cb_)
86	{}
87	void operator()() { cb(aww); }
88	};
89
90	static SmartPtr<BoundWindowCallback> recalculate_matrix_cb;
91	static SmartPtr<BoundWindowCallback> recalculate_tree_cb;
92
93	static GB_ERROR last_matrix_calculation_error = NULp;
94
95	static void matrix_changed_cb() {
96	if (matrixDisplay) {
97	matrixDisplay->mark(MatrixDisplay::NEED_SETUP);
98	matrixDisplay->update_display();
99	}
100	}
101
102	struct RecalcNeeded {
103	bool matrix;
104	bool tree;
105
106	RecalcNeeded() : matrix(false), tree(false) { }
107	};
108
109	static RecalcNeeded need_recalc;
110
111	CONSTEXPR unsigned UPDATE_DELAY = 200;
112
113	static unsigned update_cb(AW_root *aw_root);
114	inline void add_update_cb() {
115	AW_root::SINGLETON->add_timed_callback(UPDATE_DELAY, makeTimedCallback(update_cb));
116	}
117
118	inline void matrix_needs_recalc_cb() {
119	need_recalc.matrix = true;
120	add_update_cb();
121	}
122	inline void tree_needs_recalc_cb() {
123	need_recalc.tree = true;
124	add_update_cb();
125	}
126
127	inline void compressed_matrix_needs_recalc_cb() {
128	if (GLOBAL_MATRIX.has_type(DI_MATRIX_COMPRESSED)) {
129	matrix_needs_recalc_cb();
130	}
131	}
132
133	static unsigned update_cb(AW_root *aw_root) {
134	if (need_recalc.matrix) {
135	GLOBAL_MATRIX.forget();
136	need_recalc.matrix = false; // because it's forgotten
137
138	int matrix_autocalc = aw_root->awar(AWAR_DIST_MATRIX_AUTO_RECALC)->read_int();
139	if (matrix_autocalc) {
140	bool recalc_now = true;
141	int tree_autocalc = aw_root->awar(AWAR_DIST_MATRIX_AUTO_CALC_TREE)->read_int();
142	if (!tree_autocalc) recalc_now = matrixDisplay ? matrixDisplay->willShow() : false;
143
144	if (recalc_now) {
145	di_assert(recalculate_matrix_cb.isSet());
146	(*recalculate_matrix_cb)();
147	di_assert(need_recalc.tree == true);
148	}
149	}
150	di_assert(need_recalc.matrix == false);
151	}
152
153	if (need_recalc.tree) {
154	int tree_autocalc = aw_root->awar(AWAR_DIST_MATRIX_AUTO_CALC_TREE)->read_int();
155	if (tree_autocalc) {
156	di_assert(recalculate_tree_cb.isSet());
157	(*recalculate_tree_cb)();
158	need_recalc.matrix = false; // otherwise endless loop, e.g. if output-tree is used for sorting
159	}
160	}
161
162	return 0; // do not call again
163	}
164
165	static void auto_calc_changed_cb(AW_root *aw_root) {
166	int matrix_autocalc = aw_root->awar(AWAR_DIST_MATRIX_AUTO_RECALC)->read_int();
167	int tree_autocalc = aw_root->awar(AWAR_DIST_MATRIX_AUTO_CALC_TREE)->read_int();
168
169	if (matrix_autocalc && !GLOBAL_MATRIX.exists()) matrix_needs_recalc_cb();
170	if (tree_autocalc && (matrix_autocalc \|\| GLOBAL_MATRIX.exists())) tree_needs_recalc_cb();
171	}
172
173	static AW_window create_dna_matrix_window(AW_root aw_root) {
174	AW_window_simple *aws = new AW_window_simple;
175	aws->init(aw_root, "SET_DNA_MATRIX", "SET MATRIX");
176	aws->auto_increment(50, 50);
177	aws->button_length(10);
178	aws->callback(AW_POPDOWN);
179	aws->create_button("CLOSE", "CLOSE");
180
181	aws->callback(makeHelpCallback("user_matrix.hlp"));
182	aws->create_button("HELP", "HELP");
183
184	aws->at_newline();
185
186	userdef_DNA_matrix.create_input_fields(aws);
187	aws->window_fit();
188	return aws;
189	}
190
191	static void selected_tree_changed_cb() {
192	if (AW_root::SINGLETON->awar(AWAR_DIST_CORR_TRANS)->read_int() == DI_TRANSFORMATION_FROM_TREE) {
193	matrix_needs_recalc_cb();
194	}
195	}
196
197	void DI_create_matrix_variables(AW_root *aw_root, AW_default def, AW_default db) {
198	GB_transaction ta(db);
199
200	userdef_DNA_matrix.set_descriptions(AP_A, "A");
201	userdef_DNA_matrix.set_descriptions(AP_C, "C");
202	userdef_DNA_matrix.set_descriptions(AP_G, "G");
203	userdef_DNA_matrix.set_descriptions(AP_T, "TU");
204	userdef_DNA_matrix.set_descriptions(AP_GAP, "GAP");
205
206	userdef_DNA_matrix.create_awars(aw_root);
207
208	RootCallback matrix_needs_recalc_callback = makeRootCallback(matrix_needs_recalc_cb);
209	aw_root->awar_int(AWAR_DIST_MATRIX_DNA_ENABLED, 0)->add_callback(matrix_needs_recalc_callback); // user matrix disabled by default
210	{
211	GBDATA *gbd = GB_search(AW_ROOT_DEFAULT, AWAR_DIST_MATRIX_DNA_BASE, GB_FIND);
212	GB_add_callback(gbd, GB_CB_CHANGED, makeDatabaseCallback(matrix_needs_recalc_cb));
213	}
214
215	aw_root->awar_string(AWAR_DIST_WHICH_SPECIES, "marked", def)->add_callback(matrix_needs_recalc_callback);
216	{
217	char *default_ali = GBT_get_default_alignment(db);
218	aw_root->awar_string(AWAR_DIST_ALIGNMENT, "", def)->add_callback(matrix_needs_recalc_callback)->write_string(default_ali);
219	free(default_ali);
220	}
221	aw_root->awar_string(AWAR_DIST_FILTER_ALIGNMENT, "none", def);
222	aw_root->awar_string(AWAR_DIST_FILTER_NAME, "none", def);
223	aw_root->awar_string(AWAR_DIST_FILTER_FILTER, "", def)->add_callback(matrix_needs_recalc_callback);
224	aw_root->awar_int (AWAR_DIST_FILTER_SIMPLIFY, 0, def)->add_callback(matrix_needs_recalc_callback);
225
226	aw_root->awar_string(AWAR_DIST_CANCEL_CHARS, ".", def)->add_callback(matrix_needs_recalc_callback);
227	aw_root->awar_int(AWAR_DIST_CORR_TRANS, (int)DI_TRANSFORMATION_SIMILARITY, def)->add_callback(matrix_needs_recalc_callback)->set_minmax(0, DI_TRANSFORMATION_COUNT-1);
228
229	aw_root->awar(AWAR_DIST_FILTER_ALIGNMENT)->map(AWAR_DIST_ALIGNMENT);
230
231	AW_create_fileselection_awars(aw_root, AWAR_DIST_SAVE_MATRIX_BASE, ".", "", "infile");
232	aw_root->awar_int(AWAR_DIST_SAVE_MATRIX_TYPE, 0, def);
233
234	enum treetype { CURR, SORT, COMPRESS, TREEAWARCOUNT };
235	AW_awar *tree_awar[TREEAWARCOUNT] = { NULp, NULp, NULp };
236
237	aw_root->awar_string(AWAR_DIST_TREE_STD_NAME, "tree_nj", def);
238	{
239	char *currentTree = aw_root->awar_string(AWAR_TREE, "", db)->read_string();
240	tree_awar[CURR] = aw_root->awar_string(AWAR_DIST_TREE_CURR_NAME, currentTree, def);
241	tree_awar[SORT] = aw_root->awar_string(AWAR_DIST_TREE_SORT_NAME, currentTree, def);
242	free(currentTree);
243	}
244	tree_awar[COMPRESS] = aw_root->awar_string(AWAR_DIST_TREE_COMP_NAME, NO_TREE_SELECTED, def);
245
246	aw_root->awar_int(AWAR_DIST_BOOTSTRAP_COUNT, 1000, def);
247	aw_root->awar_int(AWAR_DIST_MATRIX_AUTO_RECALC, 0, def)->add_callback(auto_calc_changed_cb);
248	aw_root->awar_int(AWAR_DIST_MATRIX_AUTO_CALC_TREE, 0, def)->add_callback(auto_calc_changed_cb);
249
250	aw_root->awar_float(AWAR_DIST_MIN_DIST, 0.0)->set_minmax(0.0, 4.0);
251	aw_root->awar_float(AWAR_DIST_MAX_DIST, 0.0)->set_minmax(0.0, 4.0);
252
253	aw_root->awar_string(AWAR_SPECIES_NAME, "", db);
254
255	DI_create_cluster_awars(aw_root, def, db);
256
257	#if defined(DEBUG)
258	AWT_create_db_browser_awars(aw_root, def);
259	#endif // DEBUG
260
261	{
262	GB_push_transaction(db);
263
264	GBDATA *gb_species_data = GBT_get_species_data(db);
265	GB_add_callback(gb_species_data, GB_CB_CHANGED, makeDatabaseCallback(matrix_needs_recalc_cb));
266
267	GB_pop_transaction(db);
268	}
269
270	AWT_registerTreeAwarCallback(tree_awar[CURR], makeTreeAwarCallback(selected_tree_changed_cb), true);
271	AWT_registerTreeAwarCallback(tree_awar[SORT], makeTreeAwarCallback(matrix_needs_recalc_cb), true);
272	AWT_registerTreeAwarCallback(tree_awar[COMPRESS], makeTreeAwarCallback(compressed_matrix_needs_recalc_cb), true);
273
274	auto_calc_changed_cb(aw_root);
275	}
276
277	DI_ENTRY::DI_ENTRY(GBDATA gbd, DI_MATRIX phmatrix_)
278	: phmatrix(phmatrix_),
279	full_name(NULp),
280	sequence(NULp),
281	name(NULp),
282	group_nr(0)
283	{
284	GBDATA *gb_ali = GB_entry(gbd, phmatrix->get_aliname());
285	if (gb_ali) {
286	GBDATA *gb_data = GB_entry(gb_ali, "data");
287	if (gb_data) {
288	if (phmatrix->is_AA) {
289	sequence = new AP_sequence_simple_protein(phmatrix->get_aliview());
290	}
291	else {
292	sequence = new AP_sequence_parsimony(phmatrix->get_aliview());
293	}
294	sequence->bind_to_species(gbd);
295	sequence->lazy_load_sequence(); // load sequence
296
297	name = GBT_read_string(gbd, "name");
298	full_name = GBT_read_string(gbd, "full_name");
299	}
300	}
301	}
302
303	DI_ENTRY::DI_ENTRY(const char name_, DI_MATRIX phmatrix_)
304	: phmatrix(phmatrix_),
305	full_name(NULp),
306	sequence(NULp),
307	name(ARB_strdup(name_)),
308	group_nr(0)
309	{}
310
311	DI_ENTRY::~DI_ENTRY() {
312	delete sequence;
313	free(name);
314	free(full_name);
315	}
316
317	DI_MATRIX::DI_MATRIX(const AliView& aliview_)
318	: gb_species_data(NULp),
319	seq_len(0),
320	allocated_entries(0),
321	aliview(new AliView(aliview_)),
322	is_AA(false),
323	entries(NULp),
324	nentries(0),
325	matrix(NULp),
326	matrix_type(DI_MATRIX_FULL)
327	{
328	memset(cancel_columns, 0, sizeof(cancel_columns));
329	}
330
331	char *DI_MATRIX::unload() {
332	for (size_t i=0; i<nentries; i++) {
333	delete entries[i];
334	}
335	freenull(entries);
336	nentries = 0;
337	return NULp;
338	}
339
340	DI_MATRIX::~DI_MATRIX() {
341	unload();
342	delete matrix;
343	delete aliview;
344	}
345
346	struct TreeOrderedSpecies {
347	GBDATA *gbd;
348	int order_index;
349
350	TreeOrderedSpecies(const MatrixOrder& order, GBDATA *gb_spec)
351	: gbd(gb_spec),
352	order_index(order.get_index(GBT_read_name(gbd)))
353	{}
354	};
355
356	MatrixOrder::MatrixOrder(GBDATA *gb_main, GB_CSTR sort_tree_name)
357	: name2pos(NULp),
358	leafs(0)
359	{
360	if (sort_tree_name) {
361	int size;
362	TreeNode *sort_tree = GBT_read_tree_and_size(gb_main, sort_tree_name, new SimpleRoot, &size);
363
364	if (sort_tree) {
365	leafs = size+1;
366	name2pos = GBS_create_hash(leafs, GB_IGNORE_CASE);
367
368	IF_ASSERTION_USED(int leafsLoaded = leafs);
369	leafs = 0;
370	insert_in_hash(sort_tree);
371
372	arb_assert(leafsLoaded == leafs);
373	destroy(sort_tree);
374	}
375	else {
376	GB_clear_error();
377	}
378	}
379	}
380	static int TreeOrderedSpecies_cmp(const void p1, const void p2, void *) {
381	TreeOrderedSpecies s1 = (TreeOrderedSpecies)p1;
382	TreeOrderedSpecies s2 = (TreeOrderedSpecies)p2;
383
384	return s2->order_index - s1->order_index;
385	}
386
387	void MatrixOrder::applyTo(TreeOrderedSpecies **species_array, size_t array_size) const {
388	GB_sort((void**)species_array, 0, array_size, TreeOrderedSpecies_cmp, NULp);
389	}
390
391	GB_ERROR DI_MATRIX::load(LoadWhat what, const MatrixOrder& order, bool show_warnings, GBDATA **species_list) {
392	GBDATA *gb_main = get_gb_main();
393	const char *use = get_aliname();
394
395	GB_transaction ta(gb_main);
396
397	seq_len = GBT_get_alignment_len(gb_main, use);
398	is_AA = GBT_is_alignment_protein(gb_main, use);
399	gb_species_data = GBT_get_species_data(gb_main);
400
401	allocated_entries = 1000;
402	ARB_calloc(entries, allocated_entries);
403
404	nentries = 0;
405
406	size_t no_of_species = -1U;
407	switch (what) {
408	case DI_LOAD_ALL:
409	no_of_species = GBT_get_species_count(gb_main);
410	break;
411	case DI_LOAD_MARKED:
412	no_of_species = GBT_count_marked_species(gb_main);
413	break;
414	case DI_LOAD_LIST:
415	di_assert(species_list);
416	for (no_of_species = 0; species_list[no_of_species]; ++no_of_species) ;
417	break;
418	}
419
420	di_assert(no_of_species != -1U);
421	if (no_of_species<2) {
422	return GBS_global_string("Not enough input species (%zu)", no_of_species);
423	}
424
425	TreeOrderedSpecies *species_to_load[no_of_species];
426
427	{
428	size_t i = 0;
429	switch (what) {
430	case DI_LOAD_ALL: {
431	for (GBDATA *gb_species = GBT_first_species_rel_species_data(gb_species_data); gb_species; gb_species = GBT_next_species(gb_species), ++i) {
432	species_to_load[i] = new TreeOrderedSpecies(order, gb_species);
433	}
434	break;
435	}
436	case DI_LOAD_MARKED: {
437	for (GBDATA *gb_species = GBT_first_marked_species_rel_species_data(gb_species_data); gb_species; gb_species = GBT_next_marked_species(gb_species), ++i) {
438	species_to_load[i] = new TreeOrderedSpecies(order, gb_species);
439	}
440	break;
441	}
442	case DI_LOAD_LIST: {
443	for (i = 0; species_list[i]; ++i) {
444	species_to_load[i] = new TreeOrderedSpecies(order, species_list[i]);
445	}
446	break;
447	}
448	}
449	arb_assert(i == no_of_species);
450	}
451
452	if (order.defined()) {
453	order.applyTo(species_to_load, no_of_species);
454	if (show_warnings) {
455	int species_not_in_sort_tree = 0;
456	for (size_t i = 0; i<no_of_species; ++i) {
457	if (!species_to_load[i]->order_index) {
458	species_not_in_sort_tree++;
459	}
460	}
461	if (species_not_in_sort_tree) {
462	GBT_message(gb_main, GBS_global_string("Warning: %i of the affected species are not in sort-tree", species_not_in_sort_tree));
463	}
464	}
465	}
466	else {
467	if (show_warnings) {
468	static bool shown = false;
469	if (!shown) { // showing once is enough
470	GBT_message(gb_main, "Warning: No valid tree given to sort matrix (using default database order)");
471	shown = true;
472	}
473	}
474	}
475
476	if (no_of_species>allocated_entries) {
477	allocated_entries = no_of_species;
478	ARB_realloc(entries, allocated_entries);
479	}
480
481	GB_ERROR error = NULp;
482	arb_progress progress("Preparing sequence data", no_of_species);
483	for (size_t i = 0; i<no_of_species && !error; ++i) {
484	DI_ENTRY *phentry = new DI_ENTRY(species_to_load[i]->gbd, this);
485	if (phentry->sequence) { // a species found
486	arb_assert(nentries<allocated_entries);
487	entries[nentries++] = phentry;
488	}
489	else {
490	delete phentry;
491	}
492	delete species_to_load[i];
493	species_to_load[i] = NULp;
494
495	progress.inc_and_check_user_abort(error);
496	}
497
498	return error;
499	}
500
501	char DI_MATRIX::calculate_overall_freqs(double rel_frequencies[AP_MAX], char cancel) {
502	di_assert(is_AA == false);
503
504	long hits2[AP_MAX];
505	long sum = 0;
506	int i;
507	int pos;
508	int b;
509	long s_len = aliview->get_length();
510
511	memset((char *) &hits2[0], 0, sizeof(hits2));
512	for (size_t row = 0; row < nentries; row++) {
513	const char *seq1 = entries[row]->get_nucl_seq()->get_sequence();
514	for (pos = 0; pos < s_len; pos++) {
515	b = *(seq1++);
516	if (cancel[b]) continue;
517	hits2[b]++;
518	}
519	}
520	for (i = 0; i < AP_MAX; i++) { // LOOP_VECTORIZED
521	sum += hits2[i];
522	}
523	for (i = 0; i < AP_MAX; i++) {
524	rel_frequencies[i] = hits2[i] / (double) sum;
525	}
526	return NULp;
527	}
528
529	double DI_MATRIX::corr(double dist, double b, double & sigma) {
530	const double eps = 0.01;
531	double ar = 1.0 - dist/b;
532	sigma = 1000.0;
533	if (ar< eps) return 3.0;
534	sigma = b/ar;
535	return - b * log(1-dist/b);
536	}
537
538	GB_ERROR DI_MATRIX::calculate(const char cancel, DI_TRANSFORMATION transformation, bool aborted_flag, AP_matrix *userdef_matrix) {
539	di_assert(is_AA == false);
540
541	if (userdef_matrix) {
542	switch (transformation) {
543	case DI_TRANSFORMATION_NONE:
544	case DI_TRANSFORMATION_SIMILARITY:
545	case DI_TRANSFORMATION_JUKES_CANTOR:
546	break;
547	default:
548	aw_message("Sorry: this kind of distance correction does not support a user defined matrix - it will be ignored");
549	userdef_matrix = NULp;
550	break;
551	}
552	}
553
554	matrix = new AP_smatrix(nentries);
555
556	long s_len = aliview->get_length();
557	long hits[AP_MAX][AP_MAX];
558	size_t i;
559
560	if (nentries<=1) {
561	return "Not enough species selected to calculate matrix";
562	}
563	memset(&cancel_columns[0], 0, 256);
564
565	for (i=0; cancel[i]; i++) {
566	cancel_columns[safeCharIndex(AP_sequence_parsimony::table[safeCharIndex(cancel[i])])] = 1;
567	UNCOVERED(); // @@@ cover
568	}
569
570	long columns;
571	double b;
572	long frequencies[AP_MAX];
573	double rel_frequencies[AP_MAX];
574	double S_square = 0;
575
576	switch (transformation) {
577	case DI_TRANSFORMATION_FELSENSTEIN:
578	this->calculate_overall_freqs(rel_frequencies, cancel_columns);
579	S_square = 0.0;
580	for (i=0; i<AP_MAX; i++) S_square += rel_frequencies[i]*rel_frequencies[i];
581	break;
582	default: break;
583	};
584
585	arb_progress progress("Calculating distance matrix", matrix_halfsize(nentries, true));
586	GB_ERROR error = NULp;
587	for (size_t row = 0; row<nentries && !error; row++) {
588	for (size_t col=0; col<=row && !error; col++) {
589	columns = 0;
590
591	const unsigned char *seq1 = entries[row]->get_nucl_seq()->get_usequence();
592	const unsigned char *seq2 = entries[col]->get_nucl_seq()->get_usequence();
593
594	b = 0.0;
595	switch (transformation) {
596	case DI_TRANSFORMATION_FROM_TREE:
597	di_assert(0);
598	break;
599	case DI_TRANSFORMATION_JUKES_CANTOR:
600	b = 0.75;
601	// fall-through
602	case DI_TRANSFORMATION_NONE:
603	case DI_TRANSFORMATION_SIMILARITY: {
604	double dist = 0.0;
605	if (userdef_matrix) {
606	memset((char )hits, 0, sizeof(long) AP_MAX * AP_MAX);
607	int pos;
608	for (pos = s_len; pos >= 0; pos--) {
609	hits[(seq1++)][(seq2++)]++;
610	}
611	int x, y;
612	double diffsum = 0.0;
613	double all_sum = 0.001;
614	for (x = AP_A; x < AP_MAX; x*=2) {
615	for (y = AP_A; y < AP_MAX; y*=2) {
616	if (x==y) {
617	all_sum += hits[x][y];
618	}
619	else {
620	UNCOVERED(); // @@@ cover
621	diffsum += hits[x][y] * userdef_matrix->get(x, y);
622	all_sum += hits[x][y] * userdef_matrix->get(x, y);
623	}
624	}
625	}
626	dist = diffsum / all_sum;
627	}
628	else {
629	for (int pos = s_len; pos >= 0; pos--) {
630	int b1 = *(seq1++);
631	int b2 = *(seq2++);
632	if (cancel_columns[b1]) continue;
633	if (cancel_columns[b2]) continue;
634	columns++;
635	if (b1&b2) continue;
636	dist+=1.0;
637	}
638	if (columns == 0) columns = 1;
639	dist /= columns;
640	}
641	if (transformation==DI_TRANSFORMATION_SIMILARITY) {
642	dist = (1.0-dist);
643	}
644	else if (b) {
645	double sigma;
646	dist = this->corr(dist, b, sigma);
647	}
648	matrix->set(row, col, dist);
649	break;
650	}
651	case DI_TRANSFORMATION_KIMURA:
652	case DI_TRANSFORMATION_OLSEN:
653	case DI_TRANSFORMATION_FELSENSTEIN: {
654	int pos;
655	double dist = 0.0;
656	long N, P, Q, M;
657	double p, q;
658
659	memset((char )hits, 0, sizeof(long) AP_MAX * AP_MAX);
660	for (pos = s_len; pos >= 0; pos--) {
661	hits[(seq1++)][(seq2++)]++;
662	}
663	switch (transformation) {
664	case DI_TRANSFORMATION_KIMURA:
665	P = hits[AP_A][AP_G] +
666	hits[AP_G][AP_A] +
667	hits[AP_C][AP_T] +
668	hits[AP_T][AP_C];
669	Q = hits[AP_A][AP_C] +
670	hits[AP_A][AP_T] +
671	hits[AP_C][AP_A] +
672	hits[AP_T][AP_A] +
673	hits[AP_G][AP_C] +
674	hits[AP_G][AP_T] +
675	hits[AP_C][AP_G] +
676	hits[AP_T][AP_G];
677	M = hits[AP_A][AP_A] +
678	hits[AP_C][AP_C] +
679	hits[AP_G][AP_G] +
680	hits[AP_T][AP_T];
681	N = P+Q+M;
682	if (N==0) N=1;
683	p = (double)P/(double)N;
684	q = (double)Q/(double)N;
685	dist = - .5 * log(
686	(1.0-2.0p-q)sqrt(1.0-2.0*q)
687	);
688	break;
689
690	case DI_TRANSFORMATION_OLSEN:
691	case DI_TRANSFORMATION_FELSENSTEIN:
692
693	memset((char *)frequencies, 0,
694	sizeof(long) * AP_MAX);
695
696	N = 0;
697	M = 0;
698
699	for (i=0; i<AP_MAX; i++) {
700	if (cancel_columns[i]) continue;
701	unsigned int j;
702	for (j=0; j<i; j++) {
703	if (cancel_columns[j]) continue;
704	frequencies[i] +=
705	hits[i][j]+
706	hits[j][i];
707	}
708	frequencies[i] += hits[i][i];
709	N += frequencies[i];
710	M += hits[i][i];
711	}
712	if (N==0) N=1;
713	if (transformation == DI_TRANSFORMATION_OLSEN) { // Calc sum square freq individually for each line
714	S_square = 0.0;
715	for (i=0; i<AP_MAX; i++) S_square += frequencies[i]*frequencies[i];
716	b = 1.0 - S_square/((double)N*(double)N);
717	}
718	else {
719	b = 1.0 - S_square;
720	}
721
722	dist = ((double)(N-M)) / (double) N;
723	double sigma;
724	dist = this->corr(dist, b, sigma);
725	break;
726
727	default: return "Sorry: Transformation not implemented";
728	}
729	matrix->set(row, col, dist);
730	break;
731	}
732	default:;
733	} // switch
734	progress.inc_and_check_user_abort(error);
735	}
736	}
737	if (aborted_flag && progress.aborted()) *aborted_flag = true;
738	return error;
739	}
740
741	GB_ERROR DI_MATRIX::calculate_pro(DI_TRANSFORMATION transformation, bool *aborted_flag) {
742	di_assert(is_AA == true);
743
744	di_cattype catType;
745	switch (transformation) {
746	case DI_TRANSFORMATION_NONE: catType = NONE; break;
747	case DI_TRANSFORMATION_SIMILARITY: catType = SIMILARITY; break;
748	case DI_TRANSFORMATION_KIMURA: catType = KIMURA; break;
749	case DI_TRANSFORMATION_PAM: catType = PAM; break;
750	case DI_TRANSFORMATION_CATEGORIES_HALL: catType = HALL; break;
751	case DI_TRANSFORMATION_CATEGORIES_BARKER: catType = GEORGE; break;
752	case DI_TRANSFORMATION_CATEGORIES_CHEMICAL: catType = CHEMICAL; break;
753	default:
754	return "This correction is not available for protein data";
755	}
756	matrix = new AP_smatrix(nentries);
757
758	di_protdist prodist(UNIVERSAL, catType, nentries, entries, aliview->get_length(), matrix);
759	return prodist.makedists(aborted_flag);
760	}
761
762	typedef std::map<const char, TreeNode, charpLess> NamedNodes;
763
764	GB_ERROR link_to_tree(NamedNodes& named, TreeNode *node) {
765	GB_ERROR error = NULp;
766	if (node->is_leaf()) {
767	NamedNodes::iterator found = named.find(node->name);
768	if (found != named.end()) {
769	if (found->second) {
770	error = GBS_global_string("Invalid tree (two nodes named '%s')", node->name);
771	}
772	else {
773	found->second = node;
774	}
775	}
776	// otherwise, we do not care about the node (e.g. because it is not marked)
777	}
778	else {
779	error = link_to_tree(named, node->get_leftson());
780	if (!error) error = link_to_tree(named, node->get_rightson());
781	}
782	return error;
783	}
784
785	#if defined(ASSERTION_USED)
786	static TreeNode findNode(TreeNode node, const char *name) {
787	if (node->is_leaf()) {
788	return strcmp(node->name, name) == 0 ? node : NULp;
789	}
790
791	TreeNode *found = findNode(node->get_leftson(), name);
792	if (!found) found = findNode(node->get_rightson(), name);
793	return found;
794	}
795	#endif
796
797	static GB_ERROR init(NamedNodes& node, TreeNode tree, const DI_ENTRYconst*const entries, size_t nentries) {
798	GB_ERROR error = NULp;
799	for (size_t n = 0; n<nentries; ++n) {
800	node[entries[n]->name] = NULp;
801	}
802	error = link_to_tree(node, tree);
803	if (!error) { // check for missing species (needed but not in tree)
804	size_t missing = 0;
805	const char *exampleName = NULp;
806
807	for (size_t n = 0; n<nentries; ++n) {
808	NamedNodes::iterator found = node.find(entries[n]->name);
809	if (found == node.end()) {
810	++missing;
811	exampleName = entries[n]->name;
812	}
813	else {
814	di_assert(node[entries[n]->name] == findNode(tree, entries[n]->name));
815	if (!node[entries[n]->name]) {
816	++missing;
817	exampleName = entries[n]->name;
818	}
819	}
820	}
821
822	if (missing) {
823	error = GBS_global_string("Tree is missing %zu required species (e.g. '%s')", missing, exampleName);
824	}
825	}
826	return error;
827	}
828
829	GB_ERROR DI_MATRIX::extract_from_tree(const char treename, bool aborted_flag) {
830	GB_ERROR error = NULp;
831	if (nentries<=1) error = "Not enough species selected to calculate matrix";
832	else {
833	TreeNode *tree;
834	{
835	GB_transaction ta(get_gb_main());
836	tree = GBT_read_tree(get_gb_main(), treename, new SimpleRoot);
837	}
838	if (!tree) error = GB_await_error();
839	else {
840	arb_progress progress("Extracting distances from tree", matrix_halfsize(nentries, true));
841	NamedNodes node;
842
843	error = init(node, tree, entries, nentries);
844	matrix = new AP_smatrix(nentries);
845
846	for (size_t row = 0; row<nentries && !error; row++) {
847	TreeNode *rnode = node[entries[row]->name];
848	for (size_t col=0; col<=row && !error; col++) {
849	double dist;
850	if (col != row) {
851	TreeNode *cnode = node[entries[col]->name];
852	dist = rnode->intree_distance_to(cnode);
853	}
854	else {
855	dist = 0.0;
856	}
857	matrix->set(row, col, dist);
858	progress.inc_and_check_user_abort(error);
859	}
860	}
861	UNCOVERED();
862	destroy(tree);
863	if (aborted_flag && progress.aborted()) *aborted_flag = true;
864	if (error) progress.done();
865	}
866	}
867	return error;
868	}
869
870	__ATTR__USERESULT static GB_ERROR di_calculate_matrix(AW_root aw_root, const WeightedFilter weighted_filter, bool bootstrap_flag, bool show_warnings, bool *aborted_flag) {
871	// sets 'aborted_flag' to true, if it is non-NULp and the calculation has been aborted
872	GB_ERROR error = NULp;
873
874	if (GLOBAL_MATRIX.exists()) {
875	di_assert(!need_recalc.matrix);
876	}
877	else {
878	GB_transaction ta(GLOBAL_gb_main);
879
880	char *use = aw_root->awar(AWAR_DIST_ALIGNMENT)->read_string();
881	long ali_len = GBT_get_alignment_len(GLOBAL_gb_main, use);
882
883	if (ali_len<=0) {
884	error = "Please select a valid alignment";
885	GB_clear_error();
886	}
887	else {
888	arb_progress progress("Calculating matrix");
889	char *cancel = aw_root->awar(AWAR_DIST_CANCEL_CHARS)->read_string();
890	AliView *aliview = weighted_filter->create_aliview(use, error);
891
892	if (!error) {
893	if (bootstrap_flag) aliview->get_filter()->enable_bootstrap();
894
895	char *load_what = aw_root->awar(AWAR_DIST_WHICH_SPECIES)->read_string();
896	char *sort_tree_name = aw_root->awar(AWAR_DIST_TREE_SORT_NAME)->read_string();
897
898	LoadWhat all_flag = (strcmp(load_what, "all") == 0) ? DI_LOAD_ALL : DI_LOAD_MARKED;
899	{
900	DI_MATRIX phm = new DI_MATRIX(aliview);
901	phm->matrix_type = DI_MATRIX_FULL;
902
903	static SmartCharPtr last_sort_tree_name;
904	static SmartPtr<MatrixOrder> last_order;
905
906	if (last_sort_tree_name.isNull() \|\| !sort_tree_name \|\| strcmp(&*last_sort_tree_name, sort_tree_name) != 0) {
907	last_sort_tree_name = nulldup(sort_tree_name);
908	last_order = new MatrixOrder(GLOBAL_gb_main, sort_tree_name);
909	}
910	di_assert(last_order.isSet());
911	error = phm->load(all_flag, *last_order, show_warnings, NULp);
912
913	free(sort_tree_name);
914	error = ta.close(error);
915
916	bool aborted = false;
917	if (!error) {
918	if (progress.aborted()) {
919	phm->unload();
920	error = "Aborted by user";
921	aborted = true;
922	}
923	else {
924	DI_TRANSFORMATION trans = (DI_TRANSFORMATION)aw_root->awar(AWAR_DIST_CORR_TRANS)->read_int();
925
926	if (trans == DI_TRANSFORMATION_FROM_TREE) {
927	const char *treename = aw_root->awar(AWAR_DIST_TREE_CURR_NAME)->read_char_pntr();
928	error = phm->extract_from_tree(treename, &aborted);
929	}
930	else {
931	if (phm->is_AA) error = phm->calculate_pro(trans, &aborted);
932	else error = phm->calculate(cancel, trans, &aborted, get_user_matrix());
933	}
934	}
935	}
936
937	if (aborted) {
938	di_assert(error);
939	if (aborted_flag) *aborted_flag = true;
940	}
941	if (error) {
942	delete phm;
943	GLOBAL_MATRIX.forget();
944	}
945	else {
946	GLOBAL_MATRIX.replaceBy(phm);
947	tree_needs_recalc_cb();
948	need_recalc.matrix = false;
949	}
950	}
951	free(load_what);
952	}
953
954	free(cancel);
955	delete aliview;
956	}
957	free(use);
958
959	di_assert(contradicted(error, GLOBAL_MATRIX.exists()));
960	}
961	return error;
962	}
963
964	static void di_mark_by_distance(AW_window aww, WeightedFilter weighted_filter) {
965	AW_root *aw_root = aww->get_root();
966	float lowerBound = aw_root->awar(AWAR_DIST_MIN_DIST)->read_float();
967	float upperBound = aw_root->awar(AWAR_DIST_MAX_DIST)->read_float();
968
969	GB_ERROR error = NULp;
970	if (lowerBound >= upperBound) {
971	error = GBS_global_string("Lower bound (%f) has to be smaller than upper bound (%f)", lowerBound, upperBound);
972	}
973	else if (lowerBound<0.0 \|\| lowerBound > 1.0) {
974	error = GBS_global_string("Lower bound (%f) is not in allowed range [0.0 .. 1.0]", lowerBound);
975	}
976	else if (upperBound<0.0 \|\| upperBound > 1.0) {
977	error = GBS_global_string("Upper bound (%f) is not in allowed range [0.0 .. 1.0]", upperBound);
978	}
979	else {
980	GB_transaction ta(GLOBAL_gb_main);
981
982	char *selected = aw_root->awar(AWAR_SPECIES_NAME)->read_string();
983	if (!selected[0]) {
984	error = "Please select a species";
985	}
986	else {
987	GBDATA *gb_selected = GBT_find_species(GLOBAL_gb_main, selected);
988	if (!gb_selected) {
989	error = GBS_global_string("Couldn't find species '%s'", selected);
990	}
991	else {
992	char *use = aw_root->awar(AWAR_DIST_ALIGNMENT)->read_string();
993	char *cancel = aw_root->awar(AWAR_DIST_CANCEL_CHARS)->read_string();
994	DI_TRANSFORMATION trans = (DI_TRANSFORMATION)aw_root->awar(AWAR_DIST_CORR_TRANS)->read_int();
995	AliView *aliview = weighted_filter->create_aliview(use, error);
996
997	if (!error) {
998	DI_MATRIX *prev_global = GLOBAL_MATRIX.swap(NULp);
999
1000	size_t speciesCount = GBT_get_species_count(GLOBAL_gb_main);
1001	bool markedSelected = false;
1002
1003	arb_progress progress("Mark species by distance", speciesCount);
1004	MatrixOrder order(GLOBAL_gb_main, NULp);
1005
1006	for (GBDATA *gb_species = GBT_first_species(GLOBAL_gb_main);
1007	gb_species && !error;
1008	gb_species = GBT_next_species(gb_species))
1009	{
1010	DI_MATRIX phm = new DI_MATRIX(aliview);
1011	phm->matrix_type = DI_MATRIX_FULL;
1012	GBDATA *species_pair[] = { gb_selected, gb_species, NULp };
1013
1014	error = phm->load(DI_LOAD_LIST, order, false, species_pair);
1015
1016	if (phm->nentries == 2) { // if species has no alignment -> nentries<2
1017	if (!error) {
1018	if (phm->is_AA) error = phm->calculate_pro(trans, NULp);
1019	else error = phm->calculate(cancel, trans, NULp, get_user_matrix());
1020	}
1021
1022	if (!error) {
1023	double dist_value = phm->matrix->get(0, 1); // distance or conformance
1024	bool mark = (lowerBound <= dist_value && dist_value <= upperBound);
1025	GB_write_flag(gb_species, mark);
1026
1027	if (!markedSelected) {
1028	dist_value = phm->matrix->get(0, 0); // distance or conformance to self
1029	mark = (lowerBound <= dist_value && dist_value <= upperBound);
1030	GB_write_flag(gb_selected, mark);
1031
1032	markedSelected = true;
1033	}
1034	}
1035	}
1036
1037	delete phm;
1038	if (!error) progress.inc_and_check_user_abort(error);
1039	}
1040
1041	di_assert(!GLOBAL_MATRIX.exists());
1042	ASSERT_RESULT(DI_MATRIX*, NULp, GLOBAL_MATRIX.swap(prev_global));
1043
1044	if (error) progress.done();
1045	}
1046
1047	delete aliview;
1048	free(cancel);
1049	free(use);
1050	}
1051	}
1052
1053	free(selected);
1054	error = ta.close(error);
1055	}
1056
1057	if (error) {
1058	aw_message(error);
1059	}
1060	}
1061
1062	static GB_ERROR di_recalc_matrix() {
1063	// recalculate matrix
1064	last_matrix_calculation_error = NULp;
1065	if (need_recalc.matrix && GLOBAL_MATRIX.exists()) {
1066	GLOBAL_MATRIX.forget();
1067	}
1068	di_assert(recalculate_matrix_cb.isSet());
1069	(*recalculate_matrix_cb)();
1070	return last_matrix_calculation_error;
1071	}
1072
1073	static void di_view_matrix_cb(AW_window aww, save_matrix_params sparam) {
1074	GB_ERROR error = di_recalc_matrix();
1075	if (error) return;
1076
1077	if (!matrixDisplay) matrixDisplay = new MatrixDisplay;
1078
1079	static AW_window *viewer = NULp;
1080	if (!viewer) viewer = DI_create_view_matrix_window(aww->get_root(), matrixDisplay, sparam);
1081
1082	matrixDisplay->mark(MatrixDisplay::NEED_SETUP);
1083	matrixDisplay->update_display();
1084
1085	GLOBAL_MATRIX.set_changed_cb(matrix_changed_cb);
1086
1087	viewer->activate();
1088	}
1089
1090	static void di_save_matrix_cb(AW_window *aww) {
1091	// save the matrix
1092	GB_ERROR error = di_recalc_matrix();
1093	if (!error) {
1094	char *filename = aww->get_root()->awar(AWAR_DIST_SAVE_MATRIX_FILENAME)->read_string();
1095	enum DI_SAVE_TYPE type = (enum DI_SAVE_TYPE)aww->get_root()->awar(AWAR_DIST_SAVE_MATRIX_TYPE)->read_int();
1096
1097	GLOBAL_MATRIX.get()->save(filename, type);
1098	free(filename);
1099	}
1100	AW_refresh_fileselection(aww->get_root(), AWAR_DIST_SAVE_MATRIX_BASE);
1101	aww->hide_or_notify(error);
1102	}
1103
1104	AW_window DI_create_save_matrix_window(AW_root aw_root, save_matrix_params *save_params) {
1105	static AW_window_simple *aws = NULp;
1106	if (!aws) {
1107	aws = new AW_window_simple;
1108	aws->init(aw_root, "SAVE_MATRIX", "Save Matrix");
1109	aws->load_xfig("sel_box_user.fig");
1110
1111	aws->at("close");
1112	aws->callback(AW_POPDOWN);
1113	aws->create_button("CLOSE", "CANCEL", "C");
1114
1115
1116	aws->at("help"); aws->callback(makeHelpCallback("save_matrix.hlp"));
1117	aws->create_button("HELP", "HELP", "H");
1118
1119	aws->at("user");
1120	aws->create_option_menu(AWAR_DIST_SAVE_MATRIX_TYPE, true);
1121	aws->insert_default_option("Phylip Format (Lower Triangular Matrix)", "P", DI_SAVE_PHYLIP_COMP);
1122	aws->insert_option("Readable (using NDS)", "R", DI_SAVE_READABLE);
1123	aws->insert_option("Tabbed (using NDS)", "R", DI_SAVE_TABBED);
1124	aws->update_option_menu();
1125
1126	AW_create_standard_fileselection(aws, save_params->awar_base);
1127
1128	aws->at("save2");
1129	aws->callback(makeWindowCallback(di_save_matrix_cb));
1130	aws->create_button("SAVE", "SAVE", "S");
1131
1132	aws->at("cancel2");
1133	aws->callback(AW_POPDOWN);
1134	aws->create_button("CLOSE", "CANCEL", "C");
1135	}
1136	return aws;
1137	}
1138
1139	static AW_window awt_create_select_cancel_window(AW_root aw_root) {
1140	AW_window_simple *aws = new AW_window_simple;
1141	aws->init(aw_root, "SELECT_CHARS_TO_CANCEL_COLUMN", "CANCEL SELECT");
1142	aws->load_xfig("di_cancel.fig");
1143
1144	aws->at("close");
1145	aws->callback(AW_POPDOWN);
1146	aws->create_button("CLOSE", "CLOSE", "C");
1147
1148	aws->at("cancel");
1149	aws->create_input_field(AWAR_DIST_CANCEL_CHARS, 12);
1150
1151	return aws;
1152	}
1153
1154	static const char *enum_trans_to_string[] = {
1155	"none",
1156	"similarity",
1157	"jukes_cantor",
1158	"felsenstein",
1159
1160	"pam",
1161	"hall",
1162	"barker",
1163	"chemical",
1164
1165	"kimura",
1166	"olsen",
1167	"felsenstein voigt",
1168	"olsen voigt",
1169	"max ml",
1170
1171	NULp, // treedist
1172	};
1173
1174	STATIC_ASSERT(ARRAY_ELEMS(enum_trans_to_string) == DI_TRANSFORMATION_COUNT);
1175
1176	static void di_calculate_tree_cb(AW_window aww, WeightedFilter weighted_filter, bool bootstrap_flag) {
1177	recalculate_tree_cb = new BoundWindowCallback(aww, makeWindowCallback(di_calculate_tree_cb, weighted_filter, bootstrap_flag));
1178
1179	AW_root *aw_root = aww->get_root();
1180	GB_ERROR error = NULp;
1181	StrArray *all_names = NULp;
1182
1183	int loop_count = 0;
1184	int bootstrap_count = aw_root->awar(AWAR_DIST_BOOTSTRAP_COUNT)->read_int();
1185
1186	{
1187	char *tree_name = aw_root->awar(AWAR_DIST_TREE_STD_NAME)->read_string();
1188	error = GBT_check_tree_name(tree_name);
1189	free(tree_name);
1190	}
1191
1192	SmartPtr<arb_progress> progress;
1193	SmartPtr<ConsensusTree> ctree;
1194
1195	if (!error) {
1196	if (bootstrap_flag) {
1197	if (bootstrap_count) {
1198	progress = new arb_progress("Calculating bootstrap trees", bootstrap_count+1);
1199	}
1200	else {
1201	progress = new arb_progress("Calculating bootstrap trees (KILL to stop)", INT_MAX);
1202	}
1203	progress->auto_subtitles("tree");
1204	}
1205	else {
1206	progress = new arb_progress("Calculating tree");
1207	}
1208
1209	if (bootstrap_flag) {
1210	GLOBAL_MATRIX.forget();
1211	GLOBAL_MATRIX.set_changed_cb(NULp); // otherwise matrix window will repeatedly pop up/down
1212
1213	error = di_calculate_matrix(aw_root, weighted_filter, bootstrap_flag, true, NULp);
1214	if (!error) {
1215	DI_MATRIX *matr = GLOBAL_MATRIX.get();
1216	if (!matr) {
1217	error = "unexpected error in di_calculate_matrix_cb (data missing)";
1218	}
1219	else {
1220	all_names = new StrArray;
1221	all_names->reserve(matr->nentries+2);
1222
1223	for (size_t i=0; i<matr->nentries; i++) {
1224	all_names->put(ARB_strdup(matr->entries[i]->name));
1225	}
1226	ctree = new ConsensusTree(*all_names);
1227	}
1228	}
1229	}
1230	}
1231
1232	TreeNode *tree = NULp;
1233	do {
1234	if (error) break;
1235
1236	bool aborted = false;
1237
1238	if (bootstrap_flag) {
1239	if (loop_count>0) { // in first loop we already have a valid matrix -> no need to recalculate
1240	GLOBAL_MATRIX.forget();
1241	}
1242	}
1243	else if (need_recalc.matrix) {
1244	GLOBAL_MATRIX.forget();
1245	}
1246
1247	error = di_calculate_matrix(aw_root, weighted_filter, bootstrap_flag, !bootstrap_flag, &aborted);
1248	if (error && aborted) {
1249	error = NULp; // clear error (otherwise no tree will be read below)
1250	break; // end of bootstrap
1251	}
1252
1253	if (!GLOBAL_MATRIX.exists()) {
1254	error = "unexpected error in di_calculate_matrix_cb (data missing)";
1255	break;
1256	}
1257
1258	DI_MATRIX *matr = GLOBAL_MATRIX.get();
1259	char *names = ARB_calloc<char>(matr->nentries+2);
1260
1261	for (size_t i=0; i<matr->nentries; i++) {
1262	names[i] = matr->entries[i]->name;
1263	}
1264	di_assert(matr->nentries == matr->matrix->size());
1265	tree = neighbourjoining(names, *matr->matrix, new SimpleRoot);
1266
1267	if (bootstrap_flag) {
1268	error = ctree->insert_tree_weighted(tree, matr->nentries, 1, false);
1269	UNCOVERED();
1270	destroy(tree); tree = NULp;
1271	loop_count++;
1272	progress->inc();
1273	if (!bootstrap_count) { // when waiting for kill
1274	int t = time(NULp);
1275	static int tlast = 0;
1276
1277	if (t>tlast) {
1278	progress->force_update();
1279	tlast = t;
1280	}
1281	}
1282	}
1283	free(names);
1284	} while (bootstrap_flag && loop_count != bootstrap_count);
1285
1286	if (!error) {
1287	if (bootstrap_flag) {
1288	tree = ctree->get_consensus_tree(error);
1289	progress->inc();
1290	if (!error) {
1291	error = GBT_is_invalid(tree);
1292	di_assert(!error);
1293	}
1294	}
1295
1296	if (!error) {
1297	char *tree_name = aw_root->awar(AWAR_DIST_TREE_STD_NAME)->read_string();
1298	GB_begin_transaction(GLOBAL_gb_main);
1299	error = GBT_write_tree(GLOBAL_gb_main, tree_name, tree);
1300
1301	if (!error) {
1302	char *filter_name = AWT_get_combined_filter_name(aw_root, "dist");
1303	int transr = aw_root->awar(AWAR_DIST_CORR_TRANS)->read_int();
1304
1305	const char *comment;
1306	if (enum_trans_to_string[transr]) {
1307	comment = GBS_global_string("PRG=dnadist CORR=%s FILTER=%s PKG=ARB", enum_trans_to_string[transr], filter_name);
1308	}
1309	else {
1310	di_assert(transr == DI_TRANSFORMATION_FROM_TREE);
1311	const char *treename = aw_root->awar(AWAR_DIST_TREE_CURR_NAME)->read_char_pntr();
1312	comment = GBS_global_string("PRG=treedist (from '%s') PKG=ARB", treename);
1313	}
1314
1315	error = GBT_write_tree_remark(GLOBAL_gb_main, tree_name, comment);
1316	free(filter_name);
1317	}
1318	error = GB_end_transaction(GLOBAL_gb_main, error);
1319	free(tree_name);
1320	}
1321	}
1322
1323	UNCOVERED();
1324	destroy(tree);
1325
1326	// aw_status(); // remove 'abort' flag (@@@ got no equiv for arb_progress yet. really needed?)
1327
1328	if (bootstrap_flag) {
1329	if (all_names) delete all_names;
1330	GLOBAL_MATRIX.forget();
1331	}
1332	#if defined(DEBUG)
1333	else {
1334	di_assert(!all_names);
1335	}
1336	#endif // DEBUG
1337
1338	progress->done();
1339	if (error) {
1340	aw_message(error);
1341	}
1342	else {
1343	need_recalc.tree = false;
1344	aw_root->awar(AWAR_TREE_REFRESH)->touch();
1345	}
1346	}
1347
1348
1349	static void di_autodetect_callback(AW_window *aww) {
1350	GB_push_transaction(GLOBAL_gb_main);
1351
1352	GLOBAL_MATRIX.forget();
1353
1354	AW_root *aw_root = aww->get_root();
1355	char *use = aw_root->awar(AWAR_DIST_ALIGNMENT)->read_string();
1356	long ali_len = GBT_get_alignment_len(GLOBAL_gb_main, use);
1357	GB_ERROR error = NULp;
1358
1359	if (ali_len<=0) {
1360	GB_pop_transaction(GLOBAL_gb_main);
1361	error = "Please select a valid alignment";
1362	GB_clear_error();
1363	}
1364	else {
1365	arb_progress progress("Analyzing data");
1366
1367	char *filter_str = aw_root->awar(AWAR_DIST_FILTER_FILTER)->read_string();
1368	// char *cancel = aw_root->awar(AWAR_DIST_CANCEL_CHARS)->read_string();
1369
1370	AliView *aliview = NULp;
1371	{
1372	AP_filter *ap_filter = NULp;
1373	long flen = strlen(filter_str);
1374
1375	if (flen == ali_len) {
1376	ap_filter = new AP_filter(filter_str, "0", ali_len);
1377	}
1378	else {
1379	if (flen) {
1380	aw_message("Warning: your filter len is not equal to the alignment len\nfilter got truncated with zeros or cutted");
1381	ap_filter = new AP_filter(filter_str, "0", ali_len);
1382	}
1383	else {
1384	ap_filter = new AP_filter(ali_len); // unfiltered
1385	}
1386	}
1387
1388	error = ap_filter->is_invalid();
1389	if (!error) {
1390	AP_weights ap_weights(ap_filter);
1391	aliview = new AliView(GLOBAL_gb_main, *ap_filter, ap_weights, use);
1392	}
1393	delete ap_filter;
1394	}
1395
1396	if (error) {
1397	GB_pop_transaction(GLOBAL_gb_main);
1398	}
1399	else {
1400	DI_MATRIX phm(*aliview);
1401
1402	{
1403	char *load_what = aw_root->awar(AWAR_DIST_WHICH_SPECIES)->read_string();
1404	char *sort_tree_name = aw_root->awar(AWAR_DIST_TREE_SORT_NAME)->read_string();
1405
1406	LoadWhat all_flag = (strcmp(load_what, "all") == 0) ? DI_LOAD_ALL : DI_LOAD_MARKED;
1407
1408	GLOBAL_MATRIX.forget();
1409
1410	MatrixOrder order(GLOBAL_gb_main, sort_tree_name);
1411	error = phm.load(all_flag, order, true, NULp);
1412
1413	free(sort_tree_name);
1414	free(load_what);
1415	}
1416
1417	GB_pop_transaction(GLOBAL_gb_main);
1418
1419	if (!error) {
1420	progress.subtitle("Search Correction");
1421
1422	string msg;
1423	DI_TRANSFORMATION detected = phm.detect_transformation(msg);
1424	aw_root->awar(AWAR_DIST_CORR_TRANS)->write_int(detected);
1425	aw_message(msg.c_str());
1426	}
1427	}
1428
1429	// free(cancel);
1430	delete aliview;
1431
1432	free(filter_str);
1433	}
1434
1435	if (error) aw_message(error);
1436
1437	free(use);
1438	}
1439
1440	__ATTR__NORETURN static void di_exit(AW_window *aww) {
1441	if (GLOBAL_gb_main) {
1442	AW_root *aw_root = aww->get_root();
1443	shutdown_macro_recording(aw_root);
1444	aw_root->unlink_awars_from_DB(GLOBAL_gb_main);
1445	GB_close(GLOBAL_gb_main);
1446	}
1447	GLOBAL_MATRIX.set_changed_cb(NULp);
1448	exit(EXIT_SUCCESS);
1449	}
1450
1451	static void di_calculate_full_matrix_cb(AW_window aww, const WeightedFilter weighted_filter) {
1452	recalculate_matrix_cb = new BoundWindowCallback(aww, makeWindowCallback(di_calculate_full_matrix_cb, weighted_filter));
1453
1454	GLOBAL_MATRIX.forget_if_not_has_type(DI_MATRIX_FULL);
1455	GB_ERROR error = di_calculate_matrix(aww->get_root(), weighted_filter, 0, true, NULp);
1456	aw_message_if(error);
1457	last_matrix_calculation_error = error;
1458	if (!error) tree_needs_recalc_cb();
1459	}
1460
1461	static void di_calculate_compressed_matrix_cb(AW_window aww, WeightedFilter weighted_filter) {
1462	recalculate_matrix_cb = new BoundWindowCallback(aww, makeWindowCallback(di_calculate_compressed_matrix_cb, weighted_filter));
1463
1464	GB_transaction ta(GLOBAL_gb_main);
1465
1466	AW_root *aw_root = aww->get_root();
1467	char *treename = aw_root->awar(AWAR_DIST_TREE_COMP_NAME)->read_string();
1468	GB_ERROR error = NULp;
1469	TreeNode *tree = GBT_read_tree(GLOBAL_gb_main, treename, new SimpleRoot);
1470
1471	if (!tree) {
1472	error = GB_await_error();
1473	}
1474	else {
1475	{
1476	LocallyModify<MatrixDisplay*> skipRefresh(matrixDisplay, NULp); // skip refresh, until matrix has been compressed
1477
1478	GLOBAL_MATRIX.forget(); // always forget (as tree might have changed)
1479	error = di_calculate_matrix(aw_root, weighted_filter, 0, true, NULp);
1480	if (!error && !GLOBAL_MATRIX.exists()) {
1481	error = "Failed to calculate your matrix (bug?)";
1482	}
1483	if (!error) {
1484	error = GLOBAL_MATRIX.get()->compress(tree);
1485	}
1486	}
1487	UNCOVERED();
1488	destroy(tree);
1489
1490	// now force refresh
1491	if (matrixDisplay) {
1492	matrixDisplay->mark(MatrixDisplay::NEED_SETUP);
1493	matrixDisplay->update_display();
1494	}
1495	}
1496	free(treename);
1497	aw_message_if(error);
1498	last_matrix_calculation_error = error;
1499	if (!error) tree_needs_recalc_cb();
1500	}
1501
1502	static void di_define_sort_tree_name_cb(AW_window *aww) {
1503	AW_root *aw_root = aww->get_root();
1504	char *tree_name = aw_root->awar(AWAR_DIST_TREE_CURR_NAME)->read_string();
1505	aw_root->awar(AWAR_DIST_TREE_SORT_NAME)->write_string(tree_name);
1506	free(tree_name);
1507	}
1508	static void di_define_compression_tree_name_cb(AW_window *aww) {
1509	AW_root *aw_root = aww->get_root();
1510	char *tree_name = aw_root->awar(AWAR_DIST_TREE_CURR_NAME)->read_string();
1511	aw_root->awar(AWAR_DIST_TREE_COMP_NAME)->write_string(tree_name);
1512	free(tree_name);
1513	}
1514
1515	static void di_define_save_tree_name_cb(AW_window *aww) {
1516	AW_root *aw_root = aww->get_root();
1517	char *tree_name = aw_root->awar(AWAR_DIST_TREE_CURR_NAME)->read_string();
1518	aw_root->awar(AWAR_DIST_TREE_STD_NAME)->write_string(tree_name);
1519	free(tree_name);
1520	}
1521
1522
1523	AW_window DI_create_matrix_window(AW_root aw_root) {
1524	AW_window_simple_menu *aws = new AW_window_simple_menu;
1525	aws->init(aw_root, "NEIGHBOUR JOINING", "NEIGHBOUR JOINING [ARB_DIST]");
1526	aws->load_xfig("di_ge_ma.fig");
1527	aws->button_length(10);
1528
1529	aws->at("close");
1530	aws->callback(di_exit);
1531	aws->create_button("CLOSE", "CLOSE", "C");
1532
1533	aws->at("help");
1534	aws->callback(makeHelpCallback("dist.hlp"));
1535	aws->create_button("HELP", "HELP", "H");
1536
1537
1538	GB_push_transaction(GLOBAL_gb_main);
1539
1540	#if defined(DEBUG)
1541	AWT_create_debug_menu(aws);
1542	#endif // DEBUG
1543
1544	aws->create_menu("File", "F", AWM_ALL);
1545	insert_macro_menu_entry(aws, false);
1546	aws->insert_menu_topic("quit", "Quit", "Q", "quit.hlp", AWM_ALL, di_exit);
1547
1548	aws->create_menu("Properties", "P", AWM_ALL);
1549	aws->insert_menu_topic("frame_props", "Frame settings ...", "F", "props_frame.hlp", AWM_ALL, AW_preset_window);
1550	aws->sep______________();
1551	AW_insert_common_property_menu_entries(aws);
1552	aws->sep______________();
1553	aws->insert_menu_topic("save_props", "Save Properties (dist.arb)", "S", "savedef.hlp", AWM_ALL, AW_save_properties);
1554
1555	aws->insert_help_topic("ARB_DIST help", "D", "dist.hlp", AWM_ALL, makeHelpCallback("dist.hlp"));
1556
1557	// ------------------
1558	// left side
1559
1560	aws->at("which_species");
1561	aws->create_option_menu(AWAR_DIST_WHICH_SPECIES, true);
1562	aws->insert_option("all", "a", "all");
1563	aws->insert_default_option("marked", "m", "marked");
1564	aws->update_option_menu();
1565
1566	aws->at("which_alignment");
1567	awt_create_ALI_selection_list(GLOBAL_gb_main, (AW_window )aws, AWAR_DIST_ALIGNMENT, "=");
1568
1569	// filter & weights
1570
1571	AW_awar *awar_dist_alignment = aws->get_root()->awar_string(AWAR_DIST_ALIGNMENT);
1572	WeightedFilter *weighted_filter = // do NOT free (bound to callbacks)
1573	new WeightedFilter(GLOBAL_gb_main, aws->get_root(), AWAR_DIST_FILTER_NAME, AWAR_DIST_COLUMN_STAT_NAME, awar_dist_alignment);
1574
1575	aws->at("filter_select");
1576	aws->callback(makeCreateWindowCallback(awt_create_select_filter_win, weighted_filter->get_adfiltercbstruct()));
1577	aws->create_button("SELECT_FILTER", AWAR_DIST_FILTER_NAME);
1578
1579	aws->at("weights_select");
1580	aws->sens_mask(AWM_EXP);
1581	aws->callback(makeCreateWindowCallback(COLSTAT_create_selection_window, weighted_filter->get_column_stat()));
1582	aws->create_button("SELECT_COL_STAT", AWAR_DIST_COLUMN_STAT_NAME);
1583	aws->sens_mask(AWM_ALL);
1584
1585	aws->at("which_cancel");
1586	aws->create_input_field(AWAR_DIST_CANCEL_CHARS, 12);
1587
1588	aws->at("cancel_select");
1589	aws->callback(awt_create_select_cancel_window);
1590	aws->create_button("SELECT_CANCEL_CHARS", "Info", "C");
1591
1592	aws->at("change_matrix");
1593	aws->callback(create_dna_matrix_window);
1594	aws->create_button("EDIT_MATRIX", "Edit Matrix");
1595
1596	aws->at("enable");
1597	aws->create_toggle(AWAR_DIST_MATRIX_DNA_ENABLED);
1598
1599	aws->at("which_correction");
1600	aws->create_option_menu(AWAR_DIST_CORR_TRANS, true);
1601	aws->insert_option("none", "n", (int)DI_TRANSFORMATION_NONE);
1602	aws->insert_option("similarity", "n", (int)DI_TRANSFORMATION_SIMILARITY);
1603	aws->insert_option("jukes-cantor (dna)", "c", (int)DI_TRANSFORMATION_JUKES_CANTOR);
1604	aws->insert_option("felsenstein (dna)", "f", (int)DI_TRANSFORMATION_FELSENSTEIN);
1605	aws->insert_option("olsen (dna)", "o", (int)DI_TRANSFORMATION_OLSEN);
1606	aws->insert_option("felsenstein/voigt (exp)", "1", (int)DI_TRANSFORMATION_FELSENSTEIN_VOIGT);
1607	aws->insert_option("olsen/voigt (exp)", "2", (int)DI_TRANSFORMATION_OLSEN_VOIGT);
1608	aws->insert_option("kimura (pro)", "k", (int)DI_TRANSFORMATION_KIMURA);
1609	aws->insert_option("PAM (protein)", "c", (int)DI_TRANSFORMATION_PAM);
1610	aws->insert_option("Cat. Hall(exp)", "c", (int)DI_TRANSFORMATION_CATEGORIES_HALL);
1611	aws->insert_option("Cat. Barker(exp)", "c", (int)DI_TRANSFORMATION_CATEGORIES_BARKER);
1612	aws->insert_option("Cat.Chem (exp)", "c", (int)DI_TRANSFORMATION_CATEGORIES_CHEMICAL);
1613	aws->insert_option("from selected tree", "t", (int)DI_TRANSFORMATION_FROM_TREE);
1614	aws->insert_default_option("unknown", "u", (int)DI_TRANSFORMATION_NONE);
1615
1616	aws->update_option_menu();
1617
1618	aws->at("autodetect"); // auto
1619	aws->callback(di_autodetect_callback);
1620	aws->sens_mask(AWM_EXP);
1621	aws->create_button("AUTODETECT_CORRECTION", "AUTODETECT", "A");
1622	aws->sens_mask(AWM_ALL);
1623
1624	// -------------------
1625	// right side
1626
1627
1628	aws->at("mark_distance");
1629	aws->callback(makeWindowCallback(di_mark_by_distance, weighted_filter));
1630	aws->create_autosize_button("MARK_BY_DIST", "Mark all species");
1631
1632	aws->at("mark_lower");
1633	aws->create_input_field(AWAR_DIST_MIN_DIST, 5);
1634
1635	aws->at("mark_upper");
1636	aws->create_input_field(AWAR_DIST_MAX_DIST, 5);
1637
1638	// -----------------
1639
1640	// tree selection
1641
1642	aws->at("tree_list");
1643	awt_create_TREE_selection_list(GLOBAL_gb_main, aws, AWAR_DIST_TREE_CURR_NAME, true);
1644
1645	aws->at("detect_clusters");
1646	aws->callback(makeCreateWindowCallback(DI_create_cluster_detection_window, weighted_filter));
1647	aws->create_autosize_button("DETECT_CLUSTERS", "Detect homogenous clusters in tree", "D");
1648
1649	// matrix calculation
1650
1651	aws->button_length(18);
1652
1653	aws->at("calculate");
1654	aws->callback(makeWindowCallback(di_calculate_full_matrix_cb, weighted_filter));
1655	aws->create_button("CALC_FULL_MATRIX", "Calculate\nFull Matrix", "F");
1656
1657	aws->at("compress");
1658	aws->callback(makeWindowCallback(di_calculate_compressed_matrix_cb, weighted_filter));
1659	aws->create_button("CALC_COMPRESSED_MATRIX", "Calculate\nCompressed Matrix", "C");
1660
1661	recalculate_matrix_cb = new BoundWindowCallback(aws, makeWindowCallback(di_calculate_full_matrix_cb, weighted_filter));
1662
1663	aws->button_length(13);
1664
1665	{
1666	static save_matrix_params sparams;
1667
1668	sparams.awar_base = AWAR_DIST_SAVE_MATRIX_BASE;
1669	sparams.weighted_filter = weighted_filter;
1670
1671	aws->at("save_matrix");
1672	aws->callback(makeCreateWindowCallback(DI_create_save_matrix_window, &sparams));
1673	aws->create_button("SAVE_MATRIX", "Save matrix", "M");
1674
1675	aws->at("view_matrix");
1676	aws->callback(makeWindowCallback(di_view_matrix_cb, &sparams));
1677	aws->create_button("VIEW_MATRIX", "View matrix", "V");
1678	}
1679
1680	aws->button_length(22);
1681	aws->at("use_compr_tree");
1682	aws->callback(di_define_compression_tree_name_cb);
1683	aws->create_button("USE_COMPRESSION_TREE", "Use to compress", "");
1684	aws->at("use_sort_tree");
1685	aws->callback(di_define_sort_tree_name_cb);
1686	aws->create_button("USE_SORT_TREE", "Use to sort", "");
1687
1688	aws->at("compr_tree_name"); aws->create_input_field(AWAR_DIST_TREE_COMP_NAME, 12);
1689	aws->at("sort_tree_name"); aws->create_input_field(AWAR_DIST_TREE_SORT_NAME, 12);
1690
1691	// tree calculation
1692
1693	aws->button_length(18);
1694
1695	aws->at("t_calculate");
1696	aws->callback(makeWindowCallback(di_calculate_tree_cb, weighted_filter, false));
1697	aws->create_button("CALC_TREE", "Calculate \ntree", "C");
1698
1699	aws->at("bootstrap");
1700	aws->callback(makeWindowCallback(di_calculate_tree_cb, weighted_filter, true));
1701	aws->create_button("CALC_BOOTSTRAP_TREE", "Calculate \nbootstrap tree");
1702
1703	recalculate_tree_cb = new BoundWindowCallback(aws, makeWindowCallback(di_calculate_tree_cb, weighted_filter, false));
1704
1705	aws->button_length(22);
1706	aws->at("use_existing");
1707	aws->callback(di_define_save_tree_name_cb);
1708	aws->create_button("USE_NAME", "Use as new tree name", "");
1709
1710	aws->at("calc_tree_name");
1711	aws->create_input_field(AWAR_DIST_TREE_STD_NAME, 12);
1712
1713	aws->at("bcount");
1714	aws->create_input_field(AWAR_DIST_BOOTSTRAP_COUNT, 7);
1715
1716	{
1717	aws->sens_mask(AWM_EXP);
1718
1719	aws->at("auto_calc_tree");
1720	aws->label("Auto calculate tree");
1721	aws->create_toggle(AWAR_DIST_MATRIX_AUTO_CALC_TREE);
1722
1723	aws->at("auto_recalc");
1724	aws->label("Auto recalculate");
1725	aws->create_toggle(AWAR_DIST_MATRIX_AUTO_RECALC);
1726
1727	aws->sens_mask(AWM_ALL);
1728	}
1729
1730	bool disable_autocalc = !ARB_in_expert_mode(aw_root);
1731	if (disable_autocalc) {
1732	aw_root->awar(AWAR_DIST_MATRIX_AUTO_RECALC)->write_int(0);
1733	aw_root->awar(AWAR_DIST_MATRIX_AUTO_CALC_TREE)->write_int(0);
1734	}
1735
1736	GB_pop_transaction(GLOBAL_gb_main);
1737	return aws;
1738	}
1739
1740	// --------------------------------------------------------------------------------
1741
1742	#ifdef UNIT_TESTS
1743	#include <arb_diff.h>
1744	#include <arb_file.h>
1745
1746	#ifndef TEST_UNIT_H
1747	#include <test_unit.h>
1748	#endif
1749
1750	class DIST_testenv : virtual Noncopyable {
1751	GB_shell shell;
1752	GBDATA *gb_main;
1753	AliView *ali_view;
1754
1755	public:
1756	DIST_testenv(const char dbname, const char aliName)
1757	: ali_view(NULp)
1758	{
1759	gb_main = GB_open(dbname, "r");
1760	TEST_REJECT_NULL(gb_main);
1761
1762	GB_transaction ta(gb_main);
1763	size_t aliLength = GBT_get_alignment_len(gb_main, aliName);
1764
1765	AP_filter filter(aliLength);
1766	if (!filter.is_invalid()) {
1767	AP_weights weights(&filter);
1768	ali_view = new AliView(gb_main, filter, weights, aliName);
1769	}
1770	}
1771	~DIST_testenv() {
1772	delete ali_view;
1773	GB_close(gb_main);
1774	}
1775
1776	const AliView& aliview() const { return *ali_view; }
1777	GBDATA *gbmain() const { return gb_main; }
1778	};
1779
1780	void TEST_matrix() {
1781	for (int iat = GB_AT_RNA; iat<=GB_AT_AA; ++iat) {
1782	GB_alignment_type at = GB_alignment_type(iat);
1783	// ---------------
1784	// setup
1785	// GB_AT_RNA GB_AT_DNA GB_AT_AA
1786	const char *db_name[]= { NULp, "TEST_trees.arb", "TEST_realign.arb", "TEST_realign.arb", };
1787	const char *ali_name[]= { NULp, "ali_5s", "ali_dna", "ali_pro", };
1788
1789	TEST_ANNOTATE(GBS_global_string("ali_name=%s", ali_name[at]));
1790	DIST_testenv env(db_name[at], ali_name[at]);
1791
1792	DI_MATRIX matrix(env.aliview());
1793	MatrixOrder order(env.gbmain(), "tree_abc"); // no such tree!
1794	TEST_EXPECT_NO_ERROR(matrix.load(DI_LOAD_MARKED, order, true, NULp));
1795
1796	// -------------------------------
1797	// detect_transformation
1798	DI_TRANSFORMATION detected_trans;
1799	{
1800	string msg;
1801
1802	detected_trans = matrix.detect_transformation(msg);
1803	DI_TRANSFORMATION expected = DI_TRANSFORMATION_NONE_DETECTED;
1804	switch (at) {
1805	case GB_AT_RNA: expected = DI_TRANSFORMATION_NONE; break;
1806	case GB_AT_DNA: expected = DI_TRANSFORMATION_JUKES_CANTOR; break;
1807	case GB_AT_AA: expected = DI_TRANSFORMATION_PAM; break;
1808	case GB_AT_UNKNOWN: di_assert(0); break;
1809	}
1810	TEST_EXPECT_EQUAL(detected_trans, expected);
1811	}
1812
1813	// ------------------------------
1814	// calculate the matrix
1815
1816	// @@@ does not test user-defined transformation-matrix!
1817	if (at == GB_AT_AA) {
1818	matrix.calculate_pro(detected_trans, NULp);
1819	}
1820	else {
1821	if (at == GB_AT_RNA) detected_trans = DI_TRANSFORMATION_FELSENSTEIN; // force calculate_overall_freqs
1822	matrix.calculate("", detected_trans, NULp, NULp);
1823	}
1824
1825	// -----------------------------------
1826	// save in available formats
1827
1828	for (DI_SAVE_TYPE saveType = DI_SAVE_PHYLIP_COMP; saveType<=DI_SAVE_TABBED; saveType = DI_SAVE_TYPE(saveType+1)) {
1829	const char *savename = "distance/matrix.out";
1830	matrix.save(savename, saveType);
1831
1832	const char *suffixAT[] = { NULp, "rna", "dna", "pro" };
1833	const char *suffixST[] = { "phylipComp", "readable", "tabbed" };
1834	char *expected = GBS_global_string_copy("distance/matrix.%s.%s.expected", suffixAT[at], suffixST[saveType]);
1835
1836	// #define TEST_AUTO_UPDATE // uncomment to auto-update expected matrices
1837
1838	#if defined(TEST_AUTO_UPDATE)
1839	TEST_COPY_FILE(savename, expected);
1840	#else
1841	TEST_EXPECT_TEXTFILES_EQUAL(savename, expected);
1842	#endif // TEST_AUTO_UPDATE
1843	TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(savename));
1844
1845	free(expected);
1846	}
1847	}
1848	}
1849
1850	#endif // UNIT_TESTS
1851
1852	// --------------------------------------------------------------------------------
1853

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