added normalize.shared command

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 31da91d9276ce711814882068996d840c43cbd99..875a3c5d75b10e628ed2be7102457af2f9e4e710 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -61,6 +61,8 @@
                A7825503116519F70002E2DD /* chimerabellerophoncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerabellerophoncommand.cpp; sourceTree = "<group>"; };
                A78434881162224F00100BE0 /* chimeraccodecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraccodecommand.h; sourceTree = "<group>"; };
                A78434891162224F00100BE0 /* chimeraccodecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraccodecommand.cpp; sourceTree = "<group>"; };
+               A798626D1240D91B005FC847 /* normalizesharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = normalizesharedcommand.h; sourceTree = "<group>"; };
+               A798626E1240D91B005FC847 /* normalizesharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = normalizesharedcommand.cpp; sourceTree = "<group>"; };
                A7AE6302121C3408001DE6FC /* sharedrabundfloatvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedrabundfloatvector.h; sourceTree = "<group>"; };
                A7AE6303121C3408001DE6FC /* sharedrabundfloatvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedrabundfloatvector.cpp; sourceTree = "<group>"; };
                A7BBDA7B11B5694E006E6551 /* classifyotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = classifyotucommand.h; sourceTree = "<group>"; };
@@ -468,7 +470,7 @@
                A7DA217B113FECD400BF472F /* whittaker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = whittaker.cpp; sourceTree = "<group>"; };
                A7DA217C113FECD400BF472F /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = "<group>"; };
                A7DF0AD4121EBB14004A03EA /* clearcut.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clearcut.h; sourceTree = "<group>"; };
-               A7DF0AD5121EBB14004A03EA /* cmdargs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cmdargs.cpp; sourceTree = "<group>"; };
+               A7DF0AD5121EBB14004A03EA /* cmdargs.cpp */ = {isa = PBXFileReference; explicitFileType = sourcecode.cpp.cpp; fileEncoding = 4; path = cmdargs.cpp; sourceTree = "<group>"; };
                A7DF0AD6121EBB14004A03EA /* cmdargs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cmdargs.h; sourceTree = "<group>"; };
                A7DF0AD7121EBB14004A03EA /* common.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = common.h; sourceTree = "<group>"; };
                A7DF0AD8121EBB14004A03EA /* dayhoff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dayhoff.h; sourceTree = "<group>"; };
@@ -791,6 +793,8 @@
                                A7DA209D113FECD400BF472F /* mgclustercommand.h */,
                                A7DA20AC113FECD400BF472F /* nocommands.cpp */,
                                A7DA20AD113FECD400BF472F /* nocommands.h */,
+                               A798626D1240D91B005FC847 /* normalizesharedcommand.h */,
+                               A798626E1240D91B005FC847 /* normalizesharedcommand.cpp */,
                                A7DA20B8113FECD400BF472F /* otuhierarchycommand.cpp */,
                                A7DA20B9113FECD400BF472F /* otuhierarchycommand.h */,
                                A7DA20BC113FECD400BF472F /* parselistscommand.cpp */,

diff --git a/commandfactory.cpp b/commandfactory.cpp
index f86a354fdcb2fd4c5fb0b744f921e70cdb45abbf..8562a8d65c0f9954f68a402dac873346e6dfc444 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -85,6 +85,7 @@
 #include "sensspeccommand.h"
 #include "sffinfocommand.h"
 #include "seqerrorcommand.h"
+#include "normalizesharedcommand.h"
 
 /*******************************************************/
 
@@ -174,6 +175,7 @@ CommandFactory::CommandFactory(){
        commands["degap.seqs"]                  = "degap.seqs";
        commands["get.relabund"]                = "get.relabund";
        commands["sffinfo"]                             = "sffinfo";
+       commands["normalize.shared"]    = "normalize.shared";
        commands["classify.seqs"]               = "MPIEnabled"; 
        commands["dist.seqs"]                   = "MPIEnabled";
        commands["filter.seqs"]                 = "MPIEnabled";
@@ -306,6 +308,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "sens.spec")                             {       command = new SensSpecCommand(optionString);                            }
                else if(commandName == "seq.error")                             {       command = new SeqErrorCommand(optionString);                            }
                else if(commandName == "sffinfo")                               {       command = new SffInfoCommand(optionString);                                     }
+               else if(commandName == "normalize.shared")              {       command = new NormalizeSharedCommand(optionString);                     }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 1b3cc93f6939044c7931e3db4cafacfa8e617411..c3080d9ed8785e0b62ecb1e03f27583425beb5d9 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -220,10 +220,10 @@ int ScreenSeqsCommand::execute(){
                                numSeqsPerProcessor = numFastaSeqs / processors;
                                int startIndex =  pid * numSeqsPerProcessor;
                                if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
-                               
+                       cout << pid << '\t' << numSeqsPerProcessor << '\t' <<   startIndex << endl;
                                //align your part
                                driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
-
+                       cout << pid << " done" << endl;
                                if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos);  return 0; }
 
                                for (int i = 1; i < processors; i++) {
@@ -253,10 +253,10 @@ int ScreenSeqsCommand::execute(){
                                numSeqsPerProcessor = numFastaSeqs / processors;
                                int startIndex =  pid * numSeqsPerProcessor;
                                if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
-                               
+               cout << pid << '\t' << numSeqsPerProcessor << '\t' <<   startIndex << endl;             
                                //align your part
                                driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
-
+cout << pid << " done" << endl;
                                if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos); return 0; }
                                
                                //send bad list