X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=filterseqscommand.h;h=ed7cfd1f98ddb6f44c8c7f690447d8dea1d4f6f0;hp=af4c03a950a0f42ad4fd9d7453ad698423381bd0;hb=c48d91112209b841444923670dca5454da0e2a4d;hpb=5b7ac70116137b52dd7884b76c5bca660a5fea38

diff --git a/filterseqscommand.h b/filterseqscommand.h
index af4c03a..ed7cfd1 100644
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -1,47 +1,246 @@
-#ifndef FILTERSEQSCOMMAND_H
-#define FILTERSEQSCOMMAND_H
-
-/*
- *  filterseqscommand.h
- *  Mothur
- *
- *  Created by Thomas Ryabin on 5/4/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "command.hpp"
-#include "mothur.h"
-#include "globaldata.hpp"
-#include "readfasta.h"
-#include "readnexus.h"
-#include "readclustal.h"
-#include "readseqsphylip.h"
-
-using namespace std;
-
-class FilterSeqsCommand : public Command {
-
-public:
-	FilterSeqsCommand();
-	~FilterSeqsCommand() {};
-	int execute();	
-	
-private:
-	void doTrump();
-	void doSoft();
-	void doHard();
-	void doVertical();
-	
-	int alignmentLength;
-	int numSeqs;
-	
-	GlobalData* globaldata;	
-	ReadSeqs* readSeqs;
-	SequenceDB* db;
-	
-	string filter;
-
-};
-
-#endif
+#ifndef FILTERSEQSCOMMAND_H
+#define FILTERSEQSCOMMAND_H
+
+/*
+ *  filterseqscommand.h
+ *  Mothur
+ *
+ *  Created by Thomas Ryabin on 5/4/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "filters.h"
+
+class Sequence;
+class FilterSeqsCommand : public Command {
+
+public:
+	FilterSeqsCommand(string);
+	FilterSeqsCommand();
+	~FilterSeqsCommand() {};
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "filter.seqs";			}
+	string getCommandCategory()		{ return "Sequence Processing";	}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Filter.seqs"; }
+	string getDescription()		{ return "removes columns from alignments based on a criteria defined by the user"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
+private:
+	struct linePair {
+		unsigned long long start;
+		unsigned long long end;
+		linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
+	};
+
+	vector<linePair*> lines;
+	vector<int> processIDS;
+    map<int, vector<unsigned long long> > savedPositions;
+
+	string vertical, filter, fasta, hard, outputDir, filterFileName;
+	vector<string> fastafileNames;	
+	int alignmentLength, processors;
+	vector<int> bufferSizes;
+	vector<string> outputNames;
+
+	char trump;
+	bool abort;
+	float soft;
+	int numSeqs;
+	
+	string createFilter();
+	int filterSequences();
+	int createProcessesCreateFilter(Filters&, string);
+	int createProcessesRunFilter(string, string, string);
+	int driverRunFilter(string, string, string, linePair*);
+	int driverCreateFilter(Filters& F, string filename, linePair* line);
+	#ifdef USE_MPI
+	int driverMPIRun(int, int, MPI_File&, MPI_File&, vector<unsigned long long>&);
+	int MPICreateFilter(int, int, Filters&, MPI_File&, vector<unsigned long long>&);	
+	#endif
+	
+};
+
+
+/**************************************************************************************************/
+//custom data structure for threads to use.
+// This is passed by void pointer so it can be any data type
+// that can be passed using a single void pointer (LPVOID).
+struct filterData {
+	Filters F;
+    int count, tid, alignmentLength;
+    unsigned long long start, end;
+    MothurOut* m;
+    string filename, vertical, hard;
+    char trump;
+    float soft;
+	
+	filterData(){}
+	filterData(string fn, MothurOut* mout, unsigned long long st, unsigned long long en, int aLength, char tr, string vert, float so, string ha, int t) {
+        filename = fn;
+		m = mout;
+		start = st;
+		end = en;
+        tid = t;
+        trump = tr;
+        alignmentLength = aLength;
+        vertical = vert;
+        soft = so;
+        hard = ha;
+		count = 0;
+	}
+};
+/**************************************************************************************************/
+//custom data structure for threads to use.
+// This is passed by void pointer so it can be any data type
+// that can be passed using a single void pointer (LPVOID).
+struct filterRunData {
+    int count, tid, alignmentLength;
+    unsigned long long start, end;
+    MothurOut* m;
+    string filename;
+    string filter, outputFilename;
+	
+	filterRunData(){}
+	filterRunData(string f, string fn, string ofn, MothurOut* mout, unsigned long long st, unsigned long long en, int aLength, int t) {
+        filter = f;
+        outputFilename = ofn;
+        filename = fn;
+		m = mout;
+		start = st;
+		end = en;
+        tid = t;
+        alignmentLength = aLength;
+		count = 0;
+	}
+};
+
+/**************************************************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#else
+static DWORD WINAPI MyCreateFilterThreadFunction(LPVOID lpParam){ 
+	filterData* pDataArray;
+	pDataArray = (filterData*)lpParam;
+	
+	try {
+
+		if (pDataArray->soft != 0)			{  pDataArray->F.setSoft(pDataArray->soft);		}
+		if (pDataArray->trump != '*')		{  pDataArray->F.setTrump(pDataArray->trump);	}
+		
+		pDataArray->F.setLength(pDataArray->alignmentLength);
+		
+		if(pDataArray->trump != '*' || pDataArray->m->isTrue(pDataArray->vertical) || pDataArray->soft != 0){
+			pDataArray->F.initialize();
+		}
+		
+		if(pDataArray->hard.compare("") != 0)	{	pDataArray->F.doHard(pDataArray->hard);		}
+		else						{	pDataArray->F.setFilter(string(pDataArray->alignmentLength, '1'));	}
+        
+		ifstream in;
+		pDataArray->m->openInputFile(pDataArray->filename, in);
+        
+		//print header if you are process 0
+		if ((pDataArray->start == 0) || (pDataArray->start == 1)) {
+			in.seekg(0);
+		}else { //this accounts for the difference in line endings. 
+			in.seekg(pDataArray->start-1); pDataArray->m->gobble(in); 
+		}
+		
+		pDataArray->count = 0;
+		for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
+			
+			if (pDataArray->m->control_pressed) { in.close(); pDataArray->count = 1; return 1; }
+			
+			Sequence current(in); pDataArray->m->gobble(in); 
+			
+			if (current.getName() != "") {
+				if (current.getAligned().length() != pDataArray->alignmentLength) { pDataArray->m->mothurOut("Sequences are not all the same length, please correct."); pDataArray->m->mothurOutEndLine(); pDataArray->m->control_pressed = true;  }
+                
+                if(pDataArray->trump != '*')			{	pDataArray->F.doTrump(current);		}
+                if(pDataArray->m->isTrue(pDataArray->vertical) || pDataArray->soft != 0)	{	pDataArray->F.getFreqs(current);	}
+			}
+            pDataArray->count++;
+            //report progress
+			if((i) % 100 == 0){	pDataArray->m->mothurOutJustToScreen(toString(i)+"\n"); 		}
+		}
+		
+        if((pDataArray->count) % 100 != 0){	pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count)+"\n"); 		}
+        
+		in.close();
+		
+		return 0;
+		
+	}
+	catch(exception& e) {
+		pDataArray->m->errorOut(e, "FilterSeqsCommand", "MyCreateFilterThreadFunction");
+		exit(1);
+	}
+} 
+/**************************************************************************************************/
+static DWORD WINAPI MyRunFilterThreadFunction(LPVOID lpParam){ 
+	filterRunData* pDataArray;
+	pDataArray = (filterRunData*)lpParam;
+	
+	try {
+        
+        ofstream out;
+		pDataArray->m->openOutputFile(pDataArray->outputFilename, out);
+
+		ifstream in;
+		pDataArray->m->openInputFile(pDataArray->filename, in);
+        
+		//print header if you are process 0
+		if ((pDataArray->start == 0) || (pDataArray->start == 1)) {
+			in.seekg(0);
+		}else { //this accounts for the difference in line endings. 
+			in.seekg(pDataArray->start-1); pDataArray->m->gobble(in); 
+		}
+		
+		pDataArray->count = 0;
+		for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
+			
+			if (pDataArray->m->control_pressed) { in.close(); out.close(); pDataArray->count = 1; return 1; }
+			
+			Sequence seq(in); pDataArray->m->gobble(in);
+            if (seq.getName() != "") {
+                string align = seq.getAligned();
+                string filterSeq = "";
+                
+                for(int j=0;j<pDataArray->alignmentLength;j++){
+                    if(pDataArray->filter[j] == '1'){
+                        filterSeq += align[j];
+                    }
+                }
+                
+                out << '>' << seq.getName() << endl << filterSeq << endl;
+            }
+            pDataArray->count++;
+            //report progress
+			if((i) % 100 == 0){	pDataArray->m->mothurOutJustToScreen(toString(i)+"\n"); 		}
+		}
+		
+        if((pDataArray->count) % 100 != 0){	pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count)+"\n"); 		}
+        
+		in.close();
+        out.close();
+		
+		return 0;
+		
+	}
+	catch(exception& e) {
+		pDataArray->m->errorOut(e, "FilterSeqsCommand", "MyRunFilterThreadFunction");
+		exit(1);
+	}
+} 
+/**************************************************************************************************/
+#endif
+
+
+#endif