vertical

src/Makefile

@@ -10,12 +10,15 @@ all:	../bin/mean ../bin/json2xml \
 	../bin/mergexml \
 	../bin/manhattan \
 	../bin/groupbygene \
+	../bin/verticalize \
 	../bin/colgrep 
 
 hershey:
 	curl -s -o hershey.zip "http://paulbourke.net/dataformats/hershey/hershey.zip"
 	unzip hershey.zip hershey
 	rm hershey.zip
+../bin/verticalize:verticalize.cpp
+	$(CPP) -o $@ -Wall $< -lz
 ../bin/colgrep:colgrep.cpp
 	$(CPP) -o $@ -Wall $< -lz
 ../bin/manhattan:manhattan.cpp

src/verticalize.cpp

@@ -0,0 +1,222 @@
+/**
+ * Author:
+ *	Pierre Lindenbaum PhD
+ * Contact:
+ *	plindenbaum@yahoo.fr
+ * Date:
+ *	Oct 2011
+ * WWW:
+ *	http://plindenbaum.blogspot.com
+ * Motivation:
+ *	verticalize a table
+ * Compilation:
+ *	 g++ -o verticalize -Wall -O3 verticalize.cpp -lz
+ */
+#include <cstdlib>
+#include <vector>
+#include <map>
+#include <set>
+#include <cerrno>
+#include <string>
+#include <cstring>
+#include <stdexcept>
+#include <climits>
+#include <cmath>
+#include <cfloat>
+#include <cstdio>
+#include <iostream>
+#include <zlib.h>
+#include <sstream>
+#include <algorithm>
+#include <cassert>
+#include <stdint.h>
+
+using namespace std;
+
+
+class Verticalize
+    {
+    public:
+
+	char delim;
+	bool first_line_is_header;
+
+
+	Verticalize()
+	    {
+	    delim='\t';
+	    first_line_is_header=true;
+	    }
+	~Verticalize()
+	    {
+
+	    }
+
+	bool readline(gzFile in,std::string& line)
+	    {
+	    line.clear();
+	    int c;
+	    if(gzeof(in)) return false;
+	    while((c=gzgetc(in))!=EOF && c!='\n')
+		    {
+		    line+=(char)c;
+		    }
+	    return true;
+	    }
+	void split(const string& line,vector<string>& tokens)
+	    {
+	    size_t prev=0;
+	    size_t i=0;
+	    tokens.clear();
+	    while(i<=line.size())
+		{
+		if(i==line.size() || line[i]==delim)
+		    {
+		    tokens.push_back(line.substr(prev,i-prev));
+		    if(i==line.size()) break;
+		    prev=i+1;
+		    }
+		++i;
+		}
+	    }
+
+
+	void run(gzFile in)
+	    {
+	    size_t nLine=0UL;
+	    vector<string> header;
+	    vector<string> tokens;
+	    string line;
+	    size_t len_word=0UL;
+	    if(first_line_is_header)
+		{
+		if(!readline(in,line))
+		    {
+		    cerr << "Error cannot read first line.\n";
+		    return;
+		    }
+		++nLine;
+		split(line,header);
+		for(size_t i=0;i< header.size();++i) len_word=max(len_word,header[i].size());
+		}
+
+	    while(readline(in,line))
+		{
+		++nLine;
+		cout << ">>>"<< delim << (nLine)<< endl;
+		split(line,tokens);
+		if(first_line_is_header)
+		    {
+		    for(size_t i=0;i< header.size();++i)
+			{
+			cout << "$"<<(i+1)<< delim << header[i];
+			for(size_t j=header[i].size();j< len_word;++j)
+			    {
+			    cout << " ";
+			    }
+			cout <<delim;
+			if(i<tokens.size())
+			    {
+			    cout << tokens[i];
+			    }
+			else
+			    {
+			    cout << "???";
+			    }
+			cout <<endl;
+			}
+		    for(size_t i=header.size();i< tokens.size();++i)
+			{
+			cout << "$"<<(i+1)<<delim << "???";
+			for(size_t j=3;j< len_word;++j)
+			    {
+			    cout << " ";
+			    }
+			cout << delim << tokens[i] << endl;
+			}
+		    }
+		else
+		    {
+		    for(size_t i=header.size();i< tokens.size();++i)
+			{
+			cout << "$"<<(i+1)<<delim << tokens[i] << endl;
+			}
+		    }
+		cout << "<<<"<< delim << (nLine)<< "\n\n";
+		}
+	    }
+    };
+
+
+int main(int argc,char** argv)
+    {
+    Verticalize app;
+    int optind=1;
+    while(optind < argc)
+   		{
+   		if(std::strcmp(argv[optind],"-h")==0)
+   			{
+   			cerr << argv[0] << "Pierre Lindenbaum PHD. 2011.\n";
+   			cerr << "Compilation: "<<__DATE__<<"  at "<< __TIME__<<".\n";
+   			cerr << "Options:\n";
+   			cerr << "  -d or --delim (char) delimiter default:tab\n";
+   			cerr << "  -n first line is NOT the header.\n";
+   			cerr << "(stdin|file|file.gz)\n";
+   			exit(EXIT_FAILURE);
+   			}
+
+   		else if(std::strcmp(argv[optind],"-n")==0)
+   			{
+   			app.first_line_is_header =false;
+   			}
+   		else if((std::strcmp(argv[optind],"-d")==0 ||
+   			 std::strcmp(argv[optind],"--delim")==0)
+   			&& optind+1< argc)
+			{
+			char* p=argv[++optind];
+			if(strlen(p)!=1)
+			    {
+			    cerr << "Bad delimiter \""<< p << "\"\n";
+			    exit(EXIT_FAILURE);
+			    }
+			app.delim=p[0];
+			}
+   		else if(argv[optind][0]=='-')
+   			{
+   			fprintf(stderr,"unknown option '%s'\n",argv[optind]);
+   			exit(EXIT_FAILURE);
+   			}
+   		else
+   			{
+   			break;
+   			}
+   		++optind;
+                }
+
+    if(optind==argc)
+	    {
+	    gzFile in=gzdopen(fileno(stdin),"r");
+	    if(in==NULL)
+		{
+		cerr << "Cannot open stdin" << endl;
+		return EXIT_FAILURE;
+		}
+	    app.run(in);
+	    }
+    else
+	    {
+	    while(optind< argc)
+		{
+		char* filename=argv[optind++];
+		gzFile in=gzopen(filename,"r");
+		if(in==NULL)
+		    {
+		    cerr << "Cannot open "<< filename << " " << strerror(errno) << endl;
+		    return EXIT_FAILURE;
+		    }
+		app.run(in);
+		gzclose(in);
+		}
+	    }
+    return EXIT_SUCCESS;
+    }