print concatenated alignment for .good.nex and .bad.nex (--bisymtest-…

…remove-bad/-good)
Cibiv · Dec 18, 2018 · 0cfee46 · 0cfee46
1 parent ae96071
commit 0cfee46
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Showing 3 changed files with 34 additions and 21 deletions.
diff --git a/alignment/superalignment.cpp b/alignment/superalignment.cpp
@@ -34,13 +34,6 @@ SuperAlignment::SuperAlignment(Params &params) : Alignment()
 
     init();
 
-    if (params.print_conaln) {
-        string str = params.out_prefix;
-        str = params.out_prefix;
-        str += ".conaln";
-        printCombinedAlignment(str.c_str());
-    }
-
     cout << "Degree of missing data: " << computeMissingData() << endl;
 
 #ifdef _OPENMP
@@ -484,12 +477,12 @@ void SuperAlignment::readPartitionDir(Params &params) {
     }
 }
 
-void SuperAlignment::printPartition(const char *filename) {
+void SuperAlignment::printPartition(const char *filename, const char *aln_file) {
     try {
         ofstream out;
         out.exceptions(ios::failbit | ios::badbit);
         out.open(filename);
-        out << "#nexus" << endl << "[ partition information for alignment written in .conaln file ]" << endl
+        out << "#nexus" << endl << "[ partition information for alignment written in " << aln_file <<" file ]" << endl
         << "begin sets;" << endl;
         int part; int start_site;
         for (part = 0, start_site = 1; part < partitions.size(); part++) {
@@ -499,15 +492,23 @@ void SuperAlignment::printPartition(const char *filename) {
             out << "  charset " << name << " = " << start_site << "-" << end_site-1 << ";" << endl;
             start_site = end_site;
         }
-        out << "  charpartition mymodels =" << endl;
-        for (part = 0; part < partitions.size(); part++) {
-            string name = partitions[part]->name;
-            replace(name.begin(), name.end(), '+', '_');
-            if (part > 0) out << "," << endl;
-//            out << "    " << at(part)->getModelNameParams() << ":" << name;
-            out << "    " << partitions[part]->model_name << ":" << name;
+        bool ok_model = true;
+        for (part = 0; part < partitions.size(); part++)
+            if (partitions[part]->model_name.empty()) {
+                ok_model = false;
+                break;
+            }
+        if (ok_model) {
+            out << "  charpartition mymodels =" << endl;
+            for (part = 0; part < partitions.size(); part++) {
+                string name = partitions[part]->name;
+                replace(name.begin(), name.end(), '+', '_');
+                if (part > 0) out << "," << endl;
+    //            out << "    " << at(part)->getModelNameParams() << ":" << name;
+                out << "    " << partitions[part]->model_name << ":" << name;
+            }
+            out << ";" << endl;
         }
-        out << ";" << endl;
         out << "end;" << endl;
         out.close();
         cout << "Partition information was printed to " << filename << endl;

diff --git a/alignment/superalignment.h b/alignment/superalignment.h
@@ -76,7 +76,7 @@ class SuperAlignment : public Alignment
     /** read partition as files in a directory */
     void readPartitionDir(Params &params);
 
-    void printPartition(const char *filename);
+    void printPartition(const char *filename, const char *aln_file);
 
     void printPartitionRaxml(const char *filename);
 

diff --git a/main/phyloanalysis.cpp b/main/phyloanalysis.cpp
@@ -1951,10 +1951,19 @@ void printMiscInfo(Params &params, IQTree &iqtree, double *pattern_lh) {
         cout << "Branch lengths written to " << filename << endl;
     }
 
+    if (params.print_conaln && iqtree.isSuperTree()) {
+        string str = params.out_prefix;
+        str = params.out_prefix;
+        str += ".conaln";
+        ((SuperAlignment*)(iqtree.aln))->printCombinedAlignment(str.c_str());
+    }
+
     if (params.print_partition_info && iqtree.isSuperTree()) {
+        ASSERT(params.print_conaln);
+        string aln_file = (string)params.out_prefix + ".conaln";
         string partition_info = params.out_prefix;
         partition_info += ".partinfo.nex";
-        ((SuperAlignment*)(iqtree.aln))->printPartition(partition_info.c_str());
+        ((SuperAlignment*)(iqtree.aln))->printPartition(partition_info.c_str(), aln_file.c_str());
         partition_info = (string)params.out_prefix + ".partitions";
         ((SuperAlignment*)(iqtree.aln))->printPartitionRaxml(partition_info.c_str());
     }
@@ -3598,15 +3607,18 @@ void doSymTest(Alignment *alignment, Params &params) {
                 getSymTestID(intsym, part_id, false);
         }
         if (!part_id.empty()) {
+            SuperAlignment *saln = (SuperAlignment*)alignment;
             cout << "Removing " << part_id.size()
             << ((params.symtest == 2)? " bad" : " good") << " partitions (pvalue cutoff = "
             << params.symtest_pcutoff << ")..." << endl;
             if (part_id.size() < alignment->getNSite())
-                ((SuperAlignment*)alignment)->removePartitions(part_id);
+                saln->removePartitions(part_id);
             else
                 outError("Can't remove all partitions");
+            string aln_file = (string)params.out_prefix + ((params.symtest == 2)? ".good.phy" : ".bad.phy");
+            saln->printCombinedAlignment(aln_file.c_str());
             string filename = (string)params.out_prefix + ((params.symtest == 2)? ".good.nex" : ".bad.nex");
-            ((SuperAlignment*)alignment)->printBestPartition(filename.c_str());
+            saln->printPartition(filename.c_str(), aln_file.c_str());
         }
     }
 }