added a few evenness calculators and fixed a couple of bugs in filter.seqs and pre...

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index e319668eb770229d50a7cf15f22db7eb1e3c91c0..9966314ade99276d5d061a759be9c0fc01bc269c 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -7,10 +7,20 @@
        objects = {
 
 /* Begin PBXFileReference section */
+               7E4EBD43122018FB00D85E7B /* simpsoneven.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = simpsoneven.h; sourceTree = "<group>"; };
+               7E4EBD44122018FB00D85E7B /* simpsoneven.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = simpsoneven.cpp; sourceTree = "<group>"; };
+               7E5B28DC121FEFCC0005339C /* shannoneven.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shannoneven.h; sourceTree = "<group>"; };
+               7E5B28DD121FEFCC0005339C /* shannoneven.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shannoneven.cpp; sourceTree = "<group>"; };
+               7E5B2917121FF53C0005339C /* heip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heip.h; sourceTree = "<group>"; };
+               7E5B2918121FF53C0005339C /* heip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heip.cpp; sourceTree = "<group>"; };
+               7E5B294A121FFADC0005339C /* smithwilson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = smithwilson.h; sourceTree = "<group>"; };
+               7E5B294B121FFADC0005339C /* smithwilson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = smithwilson.cpp; sourceTree = "<group>"; };
                7E84528511EF4BEB00564975 /* seqerrorcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seqerrorcommand.h; sourceTree = "<group>"; };
                7E84528611EF4BEB00564975 /* seqerrorcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = seqerrorcommand.cpp; sourceTree = "<group>"; };
                7E85BD1C11EB5E9B00FD37C0 /* qualityscores.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = qualityscores.h; sourceTree = "<group>"; };
                7E85BD1D11EB5E9B00FD37C0 /* qualityscores.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = qualityscores.cpp; sourceTree = "<group>"; };
+               7E962A40121F76B1007464B5 /* invsimpson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = invsimpson.h; sourceTree = "<group>"; };
+               7E962A41121F76B1007464B5 /* invsimpson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = invsimpson.cpp; sourceTree = "<group>"; };
                7EA299BA11E384940022D8D3 /* sensspeccommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sensspeccommand.h; sourceTree = "<group>"; };
                7EA299BB11E384940022D8D3 /* sensspeccommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sensspeccommand.cpp; sourceTree = "<group>"; };
                7EC61A0911BEA6AF00F668D9 /* weightedlinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = weightedlinkage.cpp; sourceTree = "<group>"; };
@@ -480,6 +490,8 @@
                08FB7794FE84155DC02AAC07 /* mothur */ = {
                        isa = PBXGroup;
                        children = (
+                               7E5B28DC121FEFCC0005339C /* shannoneven.h */,
+                               7E5B28DD121FEFCC0005339C /* shannoneven.cpp */,
                                A7639F8D1175DF35008F5578 /* makefile */,
                                A7DA1FF0113FECD400BF472F /* alignment.cpp */,
                                A7DA1FF1113FECD400BF472F /* alignment.hpp */,
@@ -570,6 +582,12 @@
                A7CB593B11402EF90010EB83 /* calculators */ = {
                        isa = PBXGroup;
                        children = (
+                               7E4EBD43122018FB00D85E7B /* simpsoneven.h */,
+                               7E4EBD44122018FB00D85E7B /* simpsoneven.cpp */,
+                               7E5B294A121FFADC0005339C /* smithwilson.h */,
+                               7E5B294B121FFADC0005339C /* smithwilson.cpp */,
+                               7E962A40121F76B1007464B5 /* invsimpson.h */,
+                               7E962A41121F76B1007464B5 /* invsimpson.cpp */,
                                A7DA200B113FECD400BF472F /* calculator.cpp */,
                                A7DA200C113FECD400BF472F /* calculator.h */,
                                A7DA1FED113FECD400BF472F /* ace.h */,
@@ -684,6 +702,8 @@
                A7CB593E11402F110010EB83 /* commands */ = {
                        isa = PBXGroup;
                        children = (
+                               7E5B2917121FF53C0005339C /* heip.h */,
+                               7E5B2918121FF53C0005339C /* heip.cpp */,
                                A7DA202B113FECD400BF472F /* command.hpp */,
                                A7DA1FEF113FECD400BF472F /* aligncommand.h */,
                                A7DA1FEE113FECD400BF472F /* aligncommand.cpp */,

diff --git a/collectcommand.cpp b/collectcommand.cpp
index 8c1565b901d5b885ad86b91d31cb7cc041138535..ca48d75d276a274ff5b2259ffe211b653a02f1a9 100644 (file)
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -14,8 +14,13 @@
 #include "chao1.h"
 #include "bootstrap.h"
 #include "simpson.h"
+#include "simpsoneven.h"
+#include "invsimpson.h"
 #include "npshannon.h"
 #include "shannon.h"
+#include "smithwilson.h"
+#include "heip.h"
+#include "shannoneven.h"
 #include "jackknife.h"
 #include "geom.h"
 #include "qstat.h"
@@ -178,12 +183,27 @@ int CollectCommand::execute(){
                                        }else if (Estimators[i] == "shannon") { 
                                                cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
                                                outputNames.push_back(fileNameRoot+"shannon");
+                                       }else if (Estimators[i] == "shannoneven") { 
+                                               cDisplays.push_back(new CollectDisplay(new ShannonEven(), new OneColumnFile(fileNameRoot+"shannoneven")));
+                                               outputNames.push_back(fileNameRoot+"shannoneven");
                                        }else if (Estimators[i] == "npshannon") { 
                                                cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
                                                outputNames.push_back(fileNameRoot+"np_shannon");
+                                       }else if (Estimators[i] == "heip") { 
+                                               cDisplays.push_back(new CollectDisplay(new Heip(), new OneColumnFile(fileNameRoot+"heip")));
+                                               outputNames.push_back(fileNameRoot+"heip");
+                                       }else if (Estimators[i] == "smithwilson") { 
+                                               cDisplays.push_back(new CollectDisplay(new SmithWilson(), new OneColumnFile(fileNameRoot+"smithwilson")));
+                                               outputNames.push_back(fileNameRoot+"smithwilson");
                                        }else if (Estimators[i] == "simpson") { 
                                                cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
                                                outputNames.push_back(fileNameRoot+"simpson");
+                                       }else if (Estimators[i] == "simpsoneven") { 
+                                               cDisplays.push_back(new CollectDisplay(new SimpsonEven(), new OneColumnFile(fileNameRoot+"simpsoneven")));
+                                               outputNames.push_back(fileNameRoot+"simpsoneven");
+                                       }else if (Estimators[i] == "invsimpson") { 
+                                               cDisplays.push_back(new CollectDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+"invsimpson")));
+                                               outputNames.push_back(fileNameRoot+"invsimpson");
                                        }else if (Estimators[i] == "bootstrap") { 
                                                cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
                                                outputNames.push_back(fileNameRoot+"bootstrap");

diff --git a/heip.cpp b/heip.cpp
new file mode 100644 (file)
index 0000000..7ae285d
--- /dev/null
+++ b/heip.cpp
@@ -0,0 +1,39 @@
+/*
+ *  heip.cpp
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 8/21/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "heip.h"
+#include "shannon.h"
+
+/***********************************************************************/
+
+EstOutput Heip::getValues(SAbundVector* rank){
+       try {
+               data.resize(1,0.0000);
+               vector<double> shanData(3,0);
+               Shannon* shannon = new Shannon();
+               shanData = shannon->getValues(rank);
+               
+               long int sobs = rank->getNumBins();
+               if(sobs > 1){
+                       data[0] = (exp(shanData[0])-1) / (sobs - 1);;
+               }
+               else{
+                       data[0] = 1;
+               }
+               
+               delete shannon;
+               return data;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "Heip", "getValues");
+               exit(1);
+       }
+}
+
+/***********************************************************************/

diff --git a/heip.h b/heip.h
new file mode 100644 (file)
index 0000000..3ae115f
--- /dev/null
+++ b/heip.h
@@ -0,0 +1,27 @@
+#ifndef HEIP
+#define HEIP
+
+/*
+ *  heip.h
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 8/21/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class Heip : public Calculator  {
+       
+public:
+       Heip() : Calculator("heip", 1, false) {};
+       EstOutput getValues(SAbundVector*);
+       EstOutput getValues(vector<SharedRAbundVector*>) {return data;};
+};
+
+/***********************************************************************/
+
+#endif

diff --git a/invsimpson.cpp b/invsimpson.cpp
new file mode 100644 (file)
index 0000000..238dea6
--- /dev/null
+++ b/invsimpson.cpp
@@ -0,0 +1,42 @@
+/*
+ *  invsimpson.cpp
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 8/20/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "invsimpson.h"
+#include "simpson.h"
+
+/***********************************************************************/
+
+EstOutput InvSimpson::getValues(SAbundVector* rank){
+       try {
+               //vector<double> simpsonData(3,0);
+               data.resize(3,0);
+               vector<double> simpData(3,0);
+               Simpson* simp = new Simpson();
+               simpData = simp->getValues(rank);
+               
+               if(simpData[0] != 0){
+                       data[0] = 1/simpData[0];
+                       data[1] = 1/simpData[2];
+                       data[2] = 1/simpData[1];
+               }
+               else{
+                       data.assign(3,1);
+               }
+               
+               delete simp;
+               
+               return data;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "InvSimpson", "getValues");
+               exit(1);
+       }
+}
+
+/***********************************************************************/

diff --git a/invsimpson.h b/invsimpson.h
new file mode 100644 (file)
index 0000000..e89d8a2
--- /dev/null
+++ b/invsimpson.h
@@ -0,0 +1,29 @@
+#ifndef INVSIMPSON
+#define INVSIMPSON
+
+/*
+ *  invsimpson.h
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 8/20/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class InvSimpson : public Calculator  {
+       
+public:
+       InvSimpson() : Calculator("invsimpson", 3, false) {};
+       EstOutput getValues(SAbundVector*);
+       EstOutput getValues(vector<SharedRAbundVector*>) {return data;};
+};
+
+/***********************************************************************/
+
+#endif

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index cab29633c8528c30fe0ba032cc6d76bfea44eccb..cfa91bfeedd4334adbe8bd262e476571f61f3ece 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -306,9 +306,9 @@ void PreClusterCommand::readNameFile(){
                        in >> firstCol >> secondCol; gobble(in);
                        names[firstCol] = secondCol;
                        int size = 1;
-                       while (secondCol.find_first_of(',') != -1) { 
-                               size++;
-                               secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
+
+                       for(int i=0;i<secondCol.size();i++){
+                               if(secondCol[i] == ','){        size++; }
                        }
                        sizes[firstCol] = size;
                }

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index 217a1520bd11c3ef36e1cd48a7ed0e47326e32e8..bb9a4fd58b7362eb1ed69216cdfa2aa16817b2c6 100644 (file)
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -14,7 +14,12 @@
 #include "chao1.h"
 #include "bootstrap.h"
 #include "simpson.h"
+#include "simpsoneven.h"
+#include "heip.h"
+#include "smithwilson.h"
+#include "invsimpson.h"
 #include "npshannon.h"
+#include "shannoneven.h"
 #include "shannon.h"
 #include "jackknife.h"
 #include "coverage.h"
@@ -170,12 +175,27 @@ int RareFactCommand::execute(){
                                        }else if (Estimators[i] == "shannon") { 
                                                rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon")));
                                                outputNames.push_back(fileNameRoot+"r_shannon");
+                                       }else if (Estimators[i] == "shannoneven") { 
+                                               rDisplays.push_back(new RareDisplay(new ShannonEven(), new ThreeColumnFile(fileNameRoot+"r_shannoneven")));
+                                               outputNames.push_back(fileNameRoot+"r_shannoneven");
+                                       }else if (Estimators[i] == "heip") { 
+                                               rDisplays.push_back(new RareDisplay(new Heip(), new ThreeColumnFile(fileNameRoot+"r_heip")));
+                                               outputNames.push_back(fileNameRoot+"r_heip");
+                                       }else if (Estimators[i] == "smithwilson") { 
+                                               rDisplays.push_back(new RareDisplay(new SmithWilson(), new ThreeColumnFile(fileNameRoot+"r_smithwilson")));
+                                               outputNames.push_back(fileNameRoot+"r_smithwilson");
                                        }else if (Estimators[i] == "npshannon") { 
                                                rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon")));
                                                outputNames.push_back(fileNameRoot+"r_npshannon");
                                        }else if (Estimators[i] == "simpson") { 
                                                rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson")));
                                                outputNames.push_back(fileNameRoot+"r_simpson");
+                                       }else if (Estimators[i] == "simpsoneven") { 
+                                               rDisplays.push_back(new RareDisplay(new SimpsonEven(), new ThreeColumnFile(fileNameRoot+"r_simpsoneven")));
+                                               outputNames.push_back(fileNameRoot+"r_simpsoneven");
+                                       }else if (Estimators[i] == "invsimpson") { 
+                                               rDisplays.push_back(new RareDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+"r_invsimpson")));
+                                               outputNames.push_back(fileNameRoot+"r_invsimpson");
                                        }else if (Estimators[i] == "bootstrap") { 
                                                rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap")));
                                                outputNames.push_back(fileNameRoot+"r_bootstrap");

diff --git a/shannoneven.cpp b/shannoneven.cpp
new file mode 100644 (file)
index 0000000..77c03e7
--- /dev/null
+++ b/shannoneven.cpp
@@ -0,0 +1,40 @@
+/*
+ *  shannoneven.cpp
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 8/21/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "shannoneven.h"
+#include "shannon.h"
+
+/***********************************************************************/
+
+EstOutput ShannonEven::getValues(SAbundVector* rank){
+       try {
+               //vector<double> simpsonData(3,0);
+               data.resize(1,0);
+               vector<double> shanData(3,0);
+               Shannon* shannon = new Shannon();
+               shanData = shannon->getValues(rank);
+               
+               long int sobs = rank->getNumBins();
+               if(sobs > 1){
+                       data[0] = shanData[0] / log(sobs);
+               }
+               else{
+                       data[0] = 1;
+               }
+               
+               delete shannon;
+               return data;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ShannonEven", "getValues");
+               exit(1);
+       }
+}
+
+/***********************************************************************/

diff --git a/shannoneven.h b/shannoneven.h
new file mode 100644 (file)
index 0000000..5b03d72
--- /dev/null
+++ b/shannoneven.h
@@ -0,0 +1,27 @@
+#ifndef SHANNONEVEN
+#define SHANNONEVEN
+
+/*
+ *  shannoneven.h
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 8/21/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class ShannonEven : public Calculator  {
+       
+public:
+       ShannonEven() : Calculator("shannoneven", 1, false) {};
+       EstOutput getValues(SAbundVector*);
+       EstOutput getValues(vector<SharedRAbundVector*>) {return data;};
+};
+
+/***********************************************************************/
+
+#endif

diff --git a/simpsoneven.cpp b/simpsoneven.cpp
new file mode 100644 (file)
index 0000000..e34534a
--- /dev/null
+++ b/simpsoneven.cpp
@@ -0,0 +1,34 @@
+/*
+ *  simpsoneven.cpp
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 8/21/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "simpsoneven.h"
+#include "invsimpson.h"
+
+/***********************************************************************/
+
+EstOutput SimpsonEven::getValues(SAbundVector* rank){
+       try {
+               data.resize(1,0);
+
+               InvSimpson* simp = new InvSimpson();
+               vector<double> invSimpData = simp->getValues(rank);
+               
+               data[0] = invSimpData[0] / double(rank->getNumBins());
+               
+               
+               return data;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SimpsonEven", "getValues");
+               exit(1);
+       }
+}
+
+/***********************************************************************/
+

diff --git a/simpsoneven.h b/simpsoneven.h
new file mode 100644 (file)
index 0000000..0fb8949
--- /dev/null
+++ b/simpsoneven.h
@@ -0,0 +1,28 @@
+#ifndef SIMPSONEVEN_H
+#define SIMPSONEVEN_H
+
+/*
+ *  simpsoneven.h
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 8/21/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class SimpsonEven : public Calculator  {
+       
+public:
+       SimpsonEven() : Calculator("simpsoneven", 1, false) {};
+       EstOutput getValues(SAbundVector*);
+       EstOutput getValues(vector<SharedRAbundVector*>) {return data;};
+};
+
+/***********************************************************************/
+
+#endif
+

diff --git a/smithwilson.cpp b/smithwilson.cpp
new file mode 100644 (file)
index 0000000..ec04196
--- /dev/null
+++ b/smithwilson.cpp
@@ -0,0 +1,50 @@
+/*
+ *  smithwilson.cpp
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 8/21/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "smithwilson.h"
+
+/***********************************************************************/
+
+EstOutput SmithWilson::getValues(SAbundVector* rank){
+       try {
+
+               data.resize(1,0);
+
+               double maxRank = rank->getMaxRank();
+               double sobs = rank->getNumBins();
+               
+               double innerSum = 0;
+               for(int i=1;i<=maxRank;i++){
+                       innerSum += rank->get(i) * log(i);
+               }
+               innerSum /= sobs;
+
+               double outerSum = 0;
+               for(int i=1;i<=maxRank;i++){
+                       outerSum += rank->get(i) * (log(i) - innerSum) * (log(i) - innerSum);
+               }
+               outerSum /= sobs;
+
+               if(outerSum > 0){
+                       data[0] = 1.0000 - 2.0000 / (3.14159 * atan(outerSum));
+               }
+               else{
+                       data[0] = 1.0000;
+               }
+               
+               
+               return data;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "InvSimpson", "getValues");
+               exit(1);
+       }
+}
+
+/***********************************************************************/

diff --git a/smithwilson.h b/smithwilson.h
new file mode 100644 (file)
index 0000000..6e060d9
--- /dev/null
+++ b/smithwilson.h
@@ -0,0 +1,27 @@
+#ifndef SMITHWILSON
+#define SMITHWILSON
+
+/*
+ *  smithwilson.h
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 8/21/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class SmithWilson : public Calculator  {
+       
+public:
+       SmithWilson() : Calculator("smithwilson", 1, false) {};
+       EstOutput getValues(SAbundVector*);
+       EstOutput getValues(vector<SharedRAbundVector*>) {return data;};
+};
+
+/***********************************************************************/
+
+#endif

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 95f42626c9b324a0622c1ff99806384184d42714..087e63f58b983b092fffd09ba191665b3826a7d0 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -14,8 +14,13 @@
 #include "chao1.h"
 #include "bootstrap.h"
 #include "simpson.h"
+#include "simpsoneven.h"
+#include "invsimpson.h"
 #include "npshannon.h"
 #include "shannon.h"
+#include "heip.h"
+#include "smithwilson.h"
+#include "shannoneven.h"
 #include "jackknife.h"
 #include "geom.h"
 #include "logsd.h"
@@ -193,10 +198,20 @@ int SummaryCommand::execute(){
                                                sumCalculators.push_back(new Jackknife());
                                        }else if(Estimators[i] == "shannon"){
                                                sumCalculators.push_back(new Shannon());
+                                       }else if(Estimators[i] == "shannoneven"){
+                                               sumCalculators.push_back(new ShannonEven());
                                        }else if(Estimators[i] == "npshannon"){
                                                sumCalculators.push_back(new NPShannon());
+                                       }else if(Estimators[i] == "heip"){
+                                               sumCalculators.push_back(new Heip());
+                                       }else if(Estimators[i] == "smithwilson"){
+                                               sumCalculators.push_back(new SmithWilson());
                                        }else if(Estimators[i] == "simpson"){
                                                sumCalculators.push_back(new Simpson());
+                                       }else if(Estimators[i] == "simpsoneven"){
+                                               sumCalculators.push_back(new SimpsonEven());
+                                       }else if(Estimators[i] == "invsimpson"){
+                                               sumCalculators.push_back(new InvSimpson());
                                        }else if(Estimators[i] == "bootstrap"){
                                                sumCalculators.push_back(new Bootstrap());
                                        }else if (Estimators[i] == "nseqs") { 

diff --git a/validcalculator.cpp b/validcalculator.cpp
index 0ade87338bb9c2b264f99200a3c7e09fac3fdd12..bc8c4b8d7ab4b753cfa3f75a7c7da0b8ba740bc0 100644 (file)
--- a/validcalculator.cpp
+++ b/validcalculator.cpp
@@ -209,11 +209,16 @@ void ValidCalculators::initialSingle() {
                single["jack"]              = "jack";
                single["shannon"]           = "shannon";
                single["npshannon"]     = "npshannon";
+               single["shannoneven"]   = "shannoneven";
+               single["smithwilson"]   = "smithwilson";
+               single["heip"]                  = "heip";
                single["simpson"]           = "simpson";
+               single["simpsoneven"]   = "simpsoneven";
+               single["invsimpson"]    = "invsimpson";
                single["bergerparker"]  = "bergerparker";
                single["bootstrap"]     = "bootstrap";
                single["geometric"]     = "geometric";
-               single["logseries"]         = "logseries";
+               single["logseries"]             = "logseries";
                single["qstat"]         = "qstat";
                single["bstick"]        = "bstick";
                single["goodscoverage"] = "goodscoverage";
@@ -271,8 +276,13 @@ void ValidCalculators::initialRarefaction() {
                rarefaction["ace"]                      = "ace";
                rarefaction["jack"]                     = "jack";
                rarefaction["shannon"]          = "shannon";
+               rarefaction["smithwilson"]      = "smithwilson";
+               rarefaction["heip"]                     = "heip";
                rarefaction["npshannon"]        = "npshannon";
+               rarefaction["shannoneven"]      = "shannoneven";
                rarefaction["simpson"]          = "simpson";
+               rarefaction["invsimpson"]       = "invsimpson";
+               rarefaction["simpsoneven"]      = "simpsoneven";
                rarefaction["bootstrap"]        = "bootstrap";
                rarefaction["nseqs"]            = "nseqs";
                rarefaction["coverage"]         = "coverage";
@@ -293,8 +303,13 @@ void ValidCalculators::initialSummary() {
                summary["ace"]                  = "ace";
                summary["jack"]                 = "jack";
                summary["shannon"]              = "shannon";
+               summary["heip"]                 = "heip";
+               summary["shannoneven"]  = "shannoneven";
+               summary["smithwilson"]  = "smithwilson";
+               summary["invsimpson"]   = "invsimpson";
                summary["npshannon"]    = "npshannon";
                summary["simpson"]              = "simpson";
+               summary["simpsoneven"]  = "simpsoneven";
                summary["bergerparker"] = "bergerparker";
                summary["geometric"]    = "geometric";
                summary["bootstrap"]    = "bootstrap";