Changeset 6587

Timestamp:

09/04/10 17:39:23 (22 months ago)

Author:

westram

Message:

• species/SAI-references for alignment adaption
  • added buttons to move, delete and test references
  • changed formatting of candidate list

Location:

trunk

Files:

• MERGE/MG_adapt_ali.cxx (modified) (3 diffs)
• MERGE/MG_preserves.cxx (modified) (15 diffs)
• lib/pictures/merge/preserves.fig (modified) (2 diffs)

trunk/MERGE/MG_adapt_ali.cxx

@@ -601 +601 @@
     char     *ref_list = strdup(reference_species_names);
 
-    char *tok;
-    for (tok = strtok(ref_list, " \n,;"); tok; tok = strtok(NULL, " \n,;")) {
+    for (char *tok = strtok(ref_list, " \n,;"); tok; tok = strtok(NULL, " \n,;")) {
         bool    is_SAI           = strncmp(tok, "SAI:", 4) == 0;
         GBDATA *gb_species_left  = 0;
@@ -621 +620 @@
                                          tok,
                                          gb_species_left ? "right" : "left"));
-            continue;
-        }
-
-        // look for sequence/SAI "data"
-        GBDATA *gb_seq_left  = GBT_read_sequence(gb_species_left, alignment_name);
-        if (!gb_seq_left) continue;
-        GBDATA *gb_seq_right = GBT_read_sequence(gb_species_right, alignment_name);
-        if (!gb_seq_right) continue;
-
-        GB_TYPES type_left  = GB_read_type(gb_seq_left);
-        GB_TYPES type_right = GB_read_type(gb_seq_right);
-
-        if (type_left != type_right) {
-            aw_message(GBS_global_string("Warning: data type of '%s' differs in both databases", tok));
-            continue;
-        }
-
-        const char *warning;
-        if (type_right == GB_STRING) {
-            warning = rem->add_reference(GB_read_char_pntr(gb_seq_left), GB_read_char_pntr(gb_seq_right));
         }
         else {
-            char *sleft  = GB_read_as_string(gb_seq_left);
-            char *sright = GB_read_as_string(gb_seq_right);
-
-            warning = rem->add_reference(sleft, sright);
-
-            free(sleft);
-            free(sright);
-        }
-
-        if (warning) {
-            aw_message(GBS_global_string("Warning: '%s' %s", tok, warning));
+            // look for sequence/SAI "data"
+            GBDATA *gb_seq_left  = GBT_read_sequence(gb_species_left, alignment_name);
+            GBDATA *gb_seq_right = GBT_read_sequence(gb_species_right, alignment_name);
+
+            if (gb_seq_left && gb_seq_right) {
+                GB_TYPES type_left  = GB_read_type(gb_seq_left);
+                GB_TYPES type_right = GB_read_type(gb_seq_right);
+
+                if (type_left != type_right) {
+                    aw_message(GBS_global_string("Warning: data type of '%s' differs in both databases", tok));
+                }
+                else {
+                    const char *warning;
+                    if (type_right == GB_STRING) {
+                        warning = rem->add_reference(GB_read_char_pntr(gb_seq_left), GB_read_char_pntr(gb_seq_right));
+                    }
+                    else {
+                        char *sleft  = GB_read_as_string(gb_seq_left);
+                        char *sright = GB_read_as_string(gb_seq_right);
+
+                        warning = rem->add_reference(sleft, sright);
+
+                        free(sleft);
+                        free(sright);
+                    }
+
+                    if (warning) aw_message(GBS_global_string("Warning: '%s' %s", tok, warning));
+                }
+            }
         }
     }
@@ -685 +682 @@
 }
 
-GB_ERROR MG_transfer_sequence(MG_remap *remap, GBDATA *source_species, GBDATA *destination_species, const char *alignment_name) {
+static GB_ERROR MG_transfer_sequence(MG_remap *remap, GBDATA *source_species, GBDATA *destination_species, const char *alignment_name) {
     // align sequence after copy
     GB_ERROR error = NULL;

trunk/MERGE/MG_preserves.cxx

@@ -14 +14 @@
 
 #include "merge.hxx"
+#include "MG_adapt_ali.hxx"
 
 #include <arbdbt.h>
@@ -27 +28 @@
 // find species/SAIs to preserve alignment
 
-#define AWAR_REMAP_CANDIDATE    "tmp/merge/remap_candidates"
-#define AWAR_REMAP_ALIGNMENT    "tmp/merge/remap_alignment"
+#define AWAR_REMAP_CANDIDATE     "tmp/merge/remap_candidates"
+#define AWAR_REMAP_ALIGNMENT     "tmp/merge/remap_alignment"
+#define AWAR_REMAP_SEL_REFERENCE "tmp/merge/remap_reference"
 
 struct preserve_para {
     AW_window         *window;
-    AW_selection_list *ali_id;
-    AW_selection_list *cand_id;
+    AW_selection_list *ali_id;                      // alignments
+    AW_selection_list *cand_id;                     // reference candidates
+    AW_selection_list *ref_id;                      // used references
 };
 
@@ -61 +64 @@
 }
 
-// initialize the alignment selection list
 static void init_alignments(preserve_para *para) {
-    AW_window         *aww = para->window;
-    AW_selection_list *id  = para->ali_id;
-
-    aww->clear_selection_list(id);
-    aww->insert_default_selection(id, "All", "All");
-
-    // insert alignments available in both databases
+    // initialize the alignment selection list
     char **ali_names = get_global_alignments();
-    for (int i = 0; ali_names[i]; ++i) {
-        aww->insert_selection(id, ali_names[i], ali_names[i]);
-    }
+    para->window->init_selection_list_from_array(para->ali_id, ali_names, "All");
     GBT_free_names(ali_names);
-
-    aww->update_selection_list(id);
-    aww->get_root()->awar(AWAR_REMAP_ALIGNMENT)->write_string("All"); // select "All"
-}
-
-// clear the candidate list
+}
+
 static void clear_candidates(preserve_para *para) {
+    // clear the candidate list
     AW_window         *aww = para->window;
     AW_selection_list *id  = para->cand_id;
@@ -88 +79 @@
     aww->insert_default_selection(id, "????", "????");
     aww->update_selection_list(id);
-
-    aww->get_root()->awar(AWAR_REMAP_CANDIDATE)->write_string(""); // deselect
 }
 
@@ -135 +124 @@
 
 public:
-    Candidate(bool is_species, const char *name_, GBDATA *gb_src, GBDATA *gb_dst, const char **ali_names)
+    Candidate(bool is_species, const char *name_, GBDATA *gb_src, GBDATA *gb_dst, const char *const *ali_names)
         : name(is_species ? name_ : string("SAI:")+name_)
     {
@@ -175 +164 @@
     const char *get_name() const { return name.c_str(); }
     const char *get_entry() const {
-        bool isSAI = memcmp(get_name(), "SAI:", 4) == 0;
-        return GBS_global_string(isSAI ? "%-24s %i %li %f" : "%-8s %i %li %f",
-                                 get_name(), found_alignments, base_count_diff, score);
+        return GBS_global_string("%24s  %i %li %f", get_name(), found_alignments, base_count_diff, score);
     }
 
     bool operator < (const Candidate& other) const { // sort highest score first
         int ali_diff = found_alignments-other.found_alignments;
-
-        if (ali_diff) {
-            return ali_diff>0;
-        }
-
+        if (ali_diff) return ali_diff>0;
         return score > other.score;
     }
@@ -198 +181 @@
 
 // add all candidate species to 'candidates'
-static void find_species_candidates(Candidates& candidates, const char **ali_names) {
+static void find_species_candidates(Candidates& candidates, const char *const *ali_names) {
     aw_status("Examining species (kill to stop)");
     aw_status(0.0);
@@ -238 +221 @@
 
 // add all candidate SAIs to 'candidates'
-static void find_SAI_candidates(Candidates& candidates, const char **ali_names) {
+static void find_SAI_candidates(Candidates& candidates, const char *const *ali_names) {
     aw_status("Examining SAIs");
     aw_status(0.0);
@@ -275 +258 @@
 }
 
-// FIND button
-// (rebuild candidates list)
 static void calculate_preserves_cb(AW_window *, AW_CL cl_para) {
+    // FIND button (rebuild candidates list)
+
     GB_transaction ta1(GLOBAL_gb_merge);
     GB_transaction ta2(GLOBAL_gb_dest);
@@ -295 +278 @@
         char **ali_names = get_global_alignments();
 
-        find_SAI_candidates(candidates, const_cast<const char**>(ali_names));
-        find_species_candidates(candidates, const_cast<const char**>(ali_names));
+        find_SAI_candidates(candidates, ali_names);
+        find_species_candidates(candidates, ali_names);
 
         GBT_free_names(ali_names);
     }
     else {
-        char *ali_names[2] = { ali, 0 };
-        find_SAI_candidates(candidates, const_cast<const char**>(ali_names));
-        find_species_candidates(candidates, const_cast<const char**>(ali_names));
+        const char *ali_names[2] = { ali, 0 };
+        find_SAI_candidates(candidates, ali_names);
+        find_species_candidates(candidates, ali_names);
     }
 
@@ -326 +309 @@
 }
 
-// ADD button
-// (add current selected candidate to references)
+
+
+static char **read_references(AW_root *aw_root)  {
+    char  *ref_string = aw_root->awar(AWAR_REMAP_SPECIES_LIST)->read_string();
+    char **refs       = GBT_split_string(ref_string, " \n,;", true, NULL);
+
+    free(ref_string);
+    return refs;
+}
+static void write_references(AW_root *aw_root, const char *const *ref_array) {
+    char *ref_string = GBT_join_names(ref_array, '\n');
+    aw_root->awar(AWAR_REMAP_SPECIES_LIST)->write_string(ref_string);
+    aw_root->awar(AWAR_REMAP_ENABLE)->write_int(ref_string[0] != 0);
+    free(ref_string);
+}
+static void select_reference(AW_root *aw_root, const char *ref_to_select) {
+    aw_root->awar(AWAR_REMAP_SEL_REFERENCE)->write_string(ref_to_select);
+}
+static char *get_selected_reference(AW_root *aw_root) {
+    return aw_root->awar(AWAR_REMAP_SEL_REFERENCE)->read_string();
+}
+
+static void refresh_reference_list_cb(AW_root *aw_root, AW_CL cl_para) {
+    preserve_para  *para = (preserve_para*)cl_para;
+    char          **refs = read_references(aw_root);
+    para->window->init_selection_list_from_array(para->ref_id, refs, "");
+    GBT_free_names(refs);
+}
+
 static void add_selected_cb(AW_window *, AW_CL cl_para) {
-    preserve_para *para = (preserve_para*)cl_para;
-    AW_window     *aww  = para->window;
-    AW_root       *awr  = aww->get_root();
-
-    char *current    = awr->awar(AWAR_REMAP_CANDIDATE)->read_string();
-    char *references = awr->awar(AWAR_REMAP_SPECIES_LIST)->read_string();
-    if (references && references[0]) {
-        string ref = string(references);
-        size_t pos = ref.find(current);
-        int    len = strlen(current);
-
-        for (;
-             pos != string::npos;
-             pos = ref.find(current, pos+1))
-        {
-            if (pos == 0 || ref[pos-1] == '\n') {
-                if ((pos+len) == ref.length()) break; // at eos -> skip
-                char behind = ref[pos+len];
-                if (behind == '\n') break; // already there -> skip
-            }
-        }
-
-        if (pos == string::npos) {
-            string appended = ref+'\n'+current;
-            awr->awar(AWAR_REMAP_SPECIES_LIST)->write_string(appended.c_str());
-        }
-    }
-    else {
-        awr->awar(AWAR_REMAP_SPECIES_LIST)->write_string(current);
-    }
-
-    free(references);
-    free(current);
-
-    awr->awar(AWAR_REMAP_ENABLE)->write_int(1);
-}
-
-// CLEAR button
-// (clear references)
+    // ADD button (add currently selected candidate to references)
+
+    preserve_para *para    = (preserve_para*)cl_para;
+    AW_root       *aw_root = para->window->get_root();
+    
+    char **refs       = read_references(aw_root);
+    char  *candidate  = aw_root->awar(AWAR_REMAP_CANDIDATE)->read_string();
+    char  *selected   = get_selected_reference(aw_root);
+    int    cand_index = GBT_names_index_of(refs, candidate);
+    int    sel_index  = GBT_names_index_of(refs, selected);
+
+    if (cand_index == -1) GBT_names_add(refs, sel_index+1, candidate);
+    else                  GBT_names_move(refs, cand_index, sel_index);
+
+    write_references(aw_root, refs);
+    select_reference(aw_root, candidate);
+
+    free(selected);
+    free(candidate);
+    GBT_free_names(refs);
+
+    para->window->move_selection(para->cand_id, 1); 
+}
+
 static void clear_references_cb(AW_window *aww) {
-    AW_root *awr = aww->get_root();
-    awr->awar(AWAR_REMAP_SPECIES_LIST)->write_string("");
-    awr->awar(AWAR_REMAP_ENABLE)->write_int(0);
-}
-
-// SELECT PRESERVES window
+    // CLEAR button (clear references)
+    aww->get_root()->awar(AWAR_REMAP_SPECIES_LIST)->write_string("");
+}
+
+static void del_reference_cb(AW_window *aww) {
+    AW_root  *aw_root   = aww->get_root();
+    char    **refs      = read_references(aw_root);
+    char     *selected  = get_selected_reference(aw_root);
+    int       sel_index = GBT_names_index_of(refs, selected);
+
+    if (sel_index >= 0) {
+        select_reference(aw_root, refs[sel_index+1]);
+        GBT_names_erase(refs, sel_index);
+        write_references(aw_root, refs);
+    }
+
+    free(selected);
+    GBT_free_names(refs);
+}
+
+static void lower_reference_cb(AW_window *aww) {
+    AW_root  *aw_root   = aww->get_root();
+    char    **refs      = read_references(aw_root);
+    char     *selected  = get_selected_reference(aw_root);
+    int       sel_index = GBT_names_index_of(refs, selected);
+
+    if (sel_index >= 0) {
+        GBT_names_move(refs, sel_index, sel_index+1);
+        write_references(aw_root, refs);
+    }
+
+    free(selected);
+    GBT_free_names(refs);
+}
+static void raise_reference_cb(AW_window *aww) {
+    AW_root  *aw_root   = aww->get_root();
+    char    **refs      = read_references(aw_root);
+    char     *selected  = get_selected_reference(aw_root);
+    int       sel_index = GBT_names_index_of(refs, selected);
+
+    if (sel_index > 0) {
+        GBT_names_move(refs, sel_index, sel_index-1);
+        write_references(aw_root, refs);
+    }
+
+    free(selected);
+    GBT_free_names(refs);
+}
+
+static void test_references_cb(AW_window *aww) {
+    char           *reference_species_names = aww->get_root()->awar(AWAR_REMAP_SPECIES_LIST)->read_string();
+    GB_transaction  tm(GLOBAL_gb_merge);
+    GB_transaction  td(GLOBAL_gb_dest);
+    
+    MG_remaps test_mapping(GLOBAL_gb_merge, GLOBAL_gb_dest, true, reference_species_names); // will raise aw_message's in case of problems
+
+    free(reference_species_names);
+}
+
+static void init_preserve_awars(AW_root *aw_root) {
+    aw_root->awar_string(AWAR_REMAP_ALIGNMENT,     "", GLOBAL_gb_dest);
+    aw_root->awar_string(AWAR_REMAP_CANDIDATE,     "", GLOBAL_gb_dest);
+    aw_root->awar_string(AWAR_REMAP_SEL_REFERENCE, "", GLOBAL_gb_dest);
+}
+
 AW_window *MG_select_preserves_cb(AW_root *aw_root) {
-    aw_root->awar_string(AWAR_REMAP_ALIGNMENT, "", GLOBAL_gb_dest);
-    aw_root->awar_string(AWAR_REMAP_CANDIDATE, "", GLOBAL_gb_dest);
+    // SELECT PRESERVES window
+    init_preserve_awars(aw_root);
 
     AW_window_simple *aws = new AW_window_simple;
@@ -391 +445 @@
     aws->create_button("HELP", "HELP", "H");
 
+    // ----------
+
+    preserve_para *para = new preserve_para; // do not free (is passed to callback)
+    para->window        = aws;
+    
+    aws->at("ali");
+    para->ali_id = aws->create_selection_list(AWAR_REMAP_ALIGNMENT, 0, "", 10, 30);
+
+    // ----------
+    
     aws->at("adapt");
     aws->label("Adapt alignments");
@@ -396 +460 @@
 
     aws->at("reference");
-    aws->create_text_field(AWAR_REMAP_SPECIES_LIST);
-
-    preserve_para *para = new preserve_para; // do not free (is passed to callback)
-    para->window        = aws;
-
-    aws->at("candidate");
-    para->cand_id = aws->create_selection_list(AWAR_REMAP_CANDIDATE, 0, "", 10, 30);
-
-    aws->at("ali");
-    para->ali_id = aws->create_selection_list(AWAR_REMAP_ALIGNMENT, 0, "", 10, 30);
+    // aws->create_text_field(AWAR_REMAP_SPECIES_LIST); // @@@ needs to be a selection list!
+    para->ref_id = aws->create_selection_list(AWAR_REMAP_SEL_REFERENCE, 0, "", 10, 30);
+
+    aws->button_length(8);
+
+    aws->at("clear");
+    aws->callback(clear_references_cb);
+    aws->create_button("CLEAR", "Clear", "C");
+
+    aws->at("del");
+    aws->callback(del_reference_cb);
+    aws->create_button("DEL", "Del", "L");
+
+    aws->at("up");
+    aws->callback(raise_reference_cb);
+    aws->create_button("UP", "Up", "U");
+
+    aws->at("down");
+    aws->callback(lower_reference_cb);
+    aws->create_button("DOWN", "Down", "D");
+
+    aws->at("test");
+    aws->callback(test_references_cb);
+    aws->create_button("TEST", "Test", "T");
+    
+    // ----------
 
     aws->at("find");
@@ -411 +491 @@
     aws->create_autosize_button("FIND", "Find candidates", "F", 1);
 
+    aws->at("add");
+    aws->callback(add_selected_cb, (AW_CL)para);
+    aws->create_button("ADD", "Add", "A");
+
+    aws->at("candidate");
+    para->cand_id = aws->create_selection_list(AWAR_REMAP_CANDIDATE, 0, "", 10, 30);
+
     {
         GB_transaction ta1(GLOBAL_gb_merge);
@@ -419 +506 @@
     }
 
-    aws->button_length(8);
-
-    aws->at("add");
-    aws->callback(add_selected_cb, (AW_CL)para);
-    aws->create_button("ADD", "Add", "A");
-
-    aws->at("clear");
-    aws->callback(clear_references_cb);
-    aws->create_button("CLEAR", "Clear", "C");
+    {
+        AW_awar *awar_list = aw_root->awar(AWAR_REMAP_SPECIES_LIST);
+        awar_list->add_callback(refresh_reference_list_cb, (AW_CL)para);
+        awar_list->touch(); // trigger callback
+    }
 
     return aws;

trunk/lib/pictures/merge/preserves.fig

@@ -1 @@
-#FIG 3.2
+#FIG 3.2  Produced by xfig version 3.2.5
 Landscape
 Center
 Metric
-A4
+A4      
 100.00
 Single
@@ -15 +15 @@
          8460 7740
 2 1 0 1 0 7 50 0 -1 0.000 0 0 -1 0 0 2
-         2340 1350 7290 1350
-4 0 -1 0 0 18 12 0.0000 4 165 570 1425 975 $close\001
-4 2 -1 0 0 18 12 0.0000 4 180 465 8175 975 $help\001
-4 2 -1 0 0 18 12 0.0000 4 165 525 3690 4500 $to:ali\001
-4 1 -1 0 0 18 12 0.0000 4 180 4770 4800 1260 Find and select species/SAIs for alignment adaption\001
-4 2 -1 0 0 18 12 0.0000 4 165 1170 6705 4455 $to:reference\001
-4 0 -1 0 0 18 12 0.0000 4 165 300 1530 2475 $ali\001
-4 0 -1 0 0 18 12 0.0000 4 180 870 1530 2070 Alignment\001
-4 2 -1 0 0 18 12 0.0000 4 165 1470 8055 7560 $to:XY:candidate\001
-4 0 -1 0 0 18 12 0.0000 4 165 945 1530 5535 $candidate\001
-4 0 -1 0 0 18 12 0.0000 4 165 420 7020 2475 $add\001
-4 0 -1 0 0 18 12 0.0000 4 165 540 7020 3015 $clear\001
-4 0 -1 0 0 18 12 0.0000 4 165 945 4185 2475 $reference\001
-4 0 -1 0 0 18 12 0.0000 4 165 420 4230 5085 $find\001
-4 0 -1 0 0 18 12 0.0000 4 135 975 1530 5175 Candidates\001
-4 0 -1 0 0 18 12 0.0000 4 180 885 4185 1935 $adapt\001
-4 0 -1 0 0 18 12 0.0000 4 180 1515 4230 2115 using References\001
+         1800 1350 7740 1350
+4 0 -1 0 0 18 12 0.0000 4 210 675 1425 975 $close\001
+4 2 -1 0 0 18 12 0.0000 4 225 570 8175 975 $help\001
+4 2 -1 0 0 18 12 0.0000 4 210 645 3690 4500 $to:ali\001
+4 1 -1 0 0 18 12 0.0000 4 210 5385 4800 1260 Find and select species/SAIs for alignment adaption\001
+4 2 -1 0 0 18 12 0.0000 4 210 1380 6705 4455 $to:reference\001
+4 0 -1 0 0 18 12 0.0000 4 210 360 1530 2475 $ali\001
+4 0 -1 0 0 18 12 0.0000 4 210 1050 1530 2070 Alignment\001
+4 2 -1 0 0 18 12 0.0000 4 210 1785 8055 7560 $to:XY:candidate\001
+4 0 -1 0 0 18 12 0.0000 4 210 1140 1530 5535 $candidate\001
+4 0 -1 0 0 18 12 0.0000 4 210 1095 4185 2475 $reference\001
+4 0 -1 0 0 18 12 0.0000 4 210 510 4230 5085 $find\001
+4 0 -1 0 0 18 12 0.0000 4 165 1185 1530 5175 Candidates\001
+4 0 -1 0 0 18 12 0.0000 4 225 705 4185 1935 $adapt\001
+4 0 -1 0 0 18 12 0.0000 4 210 1815 4230 2115 using References\001
+4 0 -1 0 0 18 12 0.0000 4 210 510 7020 5085 $add\001
+4 0 -1 0 0 18 12 0.0000 4 210 630 7020 2475 $clear\001
+4 0 -1 0 0 18 12 0.0000 4 210 435 7020 2970 $del\001
+4 0 -1 0 0 18 12 0.0000 4 225 390 7020 3465 $up\001
+4 0 -1 0 0 18 12 0.0000 4 210 675 7020 3960 $down\001
+4 0 -1 0 0 18 12 0.0000 4 210 510 7020 4410 $test\001