added summary outputs for align.check

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 937959c9c1458fffd66d4af72e8525fcf0ae389d..e6d29c190433d03ead4562f963c5416e7a1f65b8 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -634,10 +634,10 @@ int ScreenSeqsCommand::getSummary(vector<unsigned long int>& positions){
                
                for (int i = 0; i < optimize.size(); i++) {
                        if (optimize[i] == "start") { startPos = startPosition[criteriaPercentile]; m->mothurOut("Optimizing start to " + toString(startPos) + "."); m->mothurOutEndLine(); }
-                       else if (optimize[i] == "end") { int endcriteriaPercentile = int(numSeqs * ((100 - criteria) / (float) 100));  endPos = endPosition[endcriteriaPercentile]; m->mothurOut("Optimizing end to " + toString(endPos) + "."); m->mothurOutEndLine();}
+                       else if (optimize[i] == "end") { int endcriteriaPercentile = int(endPosition.size() * ((100 - criteria) / (float) 100));  endPos = endPosition[endcriteriaPercentile]; m->mothurOut("Optimizing end to " + toString(endPos) + "."); m->mothurOutEndLine();}
                        else if (optimize[i] == "maxambig") { maxAmbig = ambigBases[criteriaPercentile]; m->mothurOut("Optimizing maxambig to " + toString(maxAmbig) + "."); m->mothurOutEndLine(); }
                        else if (optimize[i] == "maxhomop") { maxHomoP = longHomoPolymer[criteriaPercentile]; m->mothurOut("Optimizing maxhomop to " + toString(maxHomoP) + "."); m->mothurOutEndLine(); }
-                       else if (optimize[i] == "minlength") { int mincriteriaPercentile = int(numSeqs * ((100 - criteria) / (float) 100)); minLength = seqLength[mincriteriaPercentile]; m->mothurOut("Optimizing minlength to " + toString(minLength) + "."); m->mothurOutEndLine(); }
+                       else if (optimize[i] == "minlength") { int mincriteriaPercentile = int(seqLength.size() * ((100 - criteria) / (float) 100)); minLength = seqLength[mincriteriaPercentile]; m->mothurOut("Optimizing minlength to " + toString(minLength) + "."); m->mothurOutEndLine(); }
                        else if (optimize[i] == "maxlength") { maxLength = seqLength[criteriaPercentile]; m->mothurOut("Optimizing maxlength to " + toString(maxLength) + "."); m->mothurOutEndLine(); }
                }
 

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index 2b474c14d22389778078d6012819fd1e9f0fc7e7..ece2de0fee12364effae1b23065ef30903c22485 100644 (file)
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -186,7 +186,15 @@ int AlignCheckCommand::execute(){
                out << "name" << '\t' << "pound" << '\t' << "dash" << '\t' << "plus" << '\t' << "equal" << '\t';
                out << "loop" << '\t' << "tilde" << '\t' << "total"  << '\t' << "numseqs" << endl;
 
+               vector<int> pound;
+               vector<int> dash;
+               vector<int> plus;
+               vector<int> equal;
+               vector<int> loop;
+               vector<int> tilde;
+               vector<int> total;
                
+               int count = 0;
                while(!in.eof()){
                        if (m->control_pressed) { in.close(); out.close(); remove(outfile.c_str()); return 0; }
                        
@@ -194,7 +202,7 @@ int AlignCheckCommand::execute(){
                        if (seq.getName() != "") {
                                statData data = getStats(seq.getAligned());
                                
-                               if (haderror == 1) { break; }
+                               if (haderror == 1) { m->control_pressed = true; break; }
                                
                                int num = 1;
                                if (namefile != "") {
@@ -205,6 +213,18 @@ int AlignCheckCommand::execute(){
                                        else { num = it->second; }
                                }
                                
+                               //for each sequence this sequence represents
+                               for (int i = 0; i < num; i++) {
+                                       pound.push_back(data.pound);
+                                       dash.push_back(data.dash);
+                                       plus.push_back(data.plus);
+                                       equal.push_back(data.equal);
+                                       loop.push_back(data.loop);
+                                       tilde.push_back(data.tilde);
+                                       total.push_back(data.total);
+                               }       
+                               count++;
+                               
                                out << seq.getName() << '\t' << data.pound << '\t' << data.dash << '\t' << data.plus << '\t' << data.equal << '\t';
                                out << data.loop << '\t' << data.tilde << '\t' << data.total << '\t' << num << endl;
                        }
@@ -215,6 +235,37 @@ int AlignCheckCommand::execute(){
                
                if (m->control_pressed) {  remove(outfile.c_str()); return 0; }
                
+               sort(pound.begin(), pound.end());
+               sort(dash.begin(), dash.end());
+               sort(plus.begin(), plus.end());
+               sort(equal.begin(), equal.end());
+               sort(loop.begin(), loop.end());
+               sort(tilde.begin(), tilde.end());
+               sort(total.begin(), total.end());
+               int size = pound.size();
+               
+               int ptile0_25   = int(size * 0.025);
+               int ptile25             = int(size * 0.250);
+               int ptile50             = int(size * 0.500);
+               int ptile75             = int(size * 0.750);
+               int ptile97_5   = int(size * 0.975);
+               int ptile100    = size - 1;
+               
+               if (m->control_pressed) {  remove(outfile.c_str()); return 0; }
+               
+               m->mothurOutEndLine();
+               m->mothurOut("\t\tPound\tDash\tPlus\tEqual\tLoop\tTilde\tTotal"); m->mothurOutEndLine();
+               m->mothurOut("Minimum:\t" + toString(pound[0]) + "\t" + toString(dash[0]) + "\t" + toString(plus[0]) + "\t" + toString(equal[0]) + "\t" + toString(loop[0]) + "\t" + toString(tilde[0]) + "\t" + toString(total[0])); m->mothurOutEndLine();
+               m->mothurOut("2.5%-tile:\t" + toString(pound[ptile0_25]) + "\t" + toString(dash[ptile0_25]) + "\t" + toString(plus[ptile0_25]) + "\t" + toString(equal[ptile0_25]) + "\t"+ toString(loop[ptile0_25]) + "\t"+ toString(tilde[ptile0_25]) + "\t"+ toString(total[ptile0_25])); m->mothurOutEndLine();
+               m->mothurOut("25%-tile:\t" + toString(pound[ptile25]) + "\t" + toString(dash[ptile25]) + "\t" + toString(plus[ptile25]) + "\t" + toString(equal[ptile25]) + "\t" + toString(loop[ptile25]) + "\t" + toString(tilde[ptile25]) + "\t" + toString(total[ptile25])); m->mothurOutEndLine();
+               m->mothurOut("Median: \t" + toString(pound[ptile50]) + "\t" + toString(dash[ptile50]) + "\t" + toString(plus[ptile50]) + "\t" + toString(equal[ptile50]) + "\t" + toString(loop[ptile50]) + "\t" + toString(tilde[ptile50]) + "\t" + toString(total[ptile50])); m->mothurOutEndLine();
+               m->mothurOut("75%-tile:\t" + toString(pound[ptile75]) + "\t" + toString(dash[ptile75]) + "\t" + toString(plus[ptile75]) + "\t" + toString(equal[ptile75]) + "\t" + toString(loop[ptile75]) + "\t" + toString(tilde[ptile75]) + "\t" + toString(total[ptile75])); m->mothurOutEndLine();
+               m->mothurOut("97.5%-tile:\t" + toString(pound[ptile97_5]) + "\t" + toString(dash[ptile97_5]) + "\t" + toString(plus[ptile97_5]) + "\t" + toString(equal[ptile97_5]) + "\t" + toString(loop[ptile97_5]) + "\t" + toString(tilde[ptile97_5]) + "\t" + toString(total[ptile97_5])); m->mothurOutEndLine();
+               m->mothurOut("Maximum:\t" + toString(pound[ptile100]) + "\t" + toString(dash[ptile100]) + "\t" + toString(plus[ptile100]) + "\t" + toString(equal[ptile100]) + "\t" + toString(loop[ptile100]) + "\t" + toString(tilde[ptile100]) + "\t" + toString(total[ptile100])); m->mothurOutEndLine();
+               if (namefile == "") {  m->mothurOut("# of Seqs:\t" + toString(count)); m->mothurOutEndLine(); }
+               else { m->mothurOut("# of unique seqs:\t" + toString(count)); m->mothurOutEndLine(); m->mothurOut("total # of seqs:\t" + toString(size)); m->mothurOutEndLine(); }
+               
+               
                m->mothurOutEndLine();
                m->mothurOut("Output File Name: "); m->mothurOutEndLine();
                m->mothurOut(outfile); m->mothurOutEndLine();   outputNames.push_back(outfile); outputTypes["aligncheck"].push_back(outfile);

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index c0f91969eda2277e4c8b02c3a78db2a7390716fe..8c13e7fbbd76895b751ae982b8df9a093e1c1ca9 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -328,13 +328,14 @@ int SeqSummaryCommand::execute(){
                sort(seqLength.begin(), seqLength.end());
                sort(ambigBases.begin(), ambigBases.end());
                sort(longHomoPolymer.begin(), longHomoPolymer.end());
-               
-               int ptile0_25   = int(numSeqs * 0.025);
-               int ptile25             = int(numSeqs * 0.250);
-               int ptile50             = int(numSeqs * 0.500);
-               int ptile75             = int(numSeqs * 0.750);
-               int ptile97_5   = int(numSeqs * 0.975);
-               int ptile100    = numSeqs - 1;
+               int size = startPosition.size();
+                               
+               int ptile0_25   = int(size * 0.025);
+               int ptile25             = int(size * 0.250);
+               int ptile50             = int(size * 0.500);
+               int ptile75             = int(size * 0.750);
+               int ptile97_5   = int(size * 0.975);
+               int ptile100    = size - 1;
                
                //to compensate for blank sequences that would result in startPosition and endPostion equalling -1
                if (startPosition[0] == -1) {  startPosition[0] = 0;    }