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375873950F7D61240040F377 /* nocommands.cpp */,
375873960F7D61240040F377 /* nocommands.h */,
375873970F7D61240040F377 /* nseqs.h */,
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- 375873990F7D61240040F377 /* sharedanderberg.h */,
3758739A0F7D61240040F377 /* sharedbraycurtis.cpp */,
3758739B0F7D61240040F377 /* sharedbraycurtis.h */,
3758739C0F7D61240040F377 /* sharedkulczynski.cpp */,
37D9281E0F21331F001D4494 /* shannon.cpp */,
37D928230F21331F001D4494 /* sharedace.h */,
37D928220F21331F001D4494 /* sharedace.cpp */,
- 375873FA0F7D64D20040F377 /* sharedanderberg.h */,
- 375873E20F7D63B50040F377 /* sharedanderberg.cpp */,
375873FB0F7D64DA0040F377 /* sharedbraycurtis.h */,
375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */,
EB6F01590F6AC1670048081A /* sharedbdiversity.h */,
375873AA0F7D61240040F377 /* heatmapcommand.cpp in Sources */,
375873AB0F7D61240040F377 /* libshuffcommand.cpp in Sources */,
375873AC0F7D61240040F377 /* nocommands.cpp in Sources */,
- 375873AD0F7D61240040F377 /* sharedanderberg.cpp in Sources */,
375873AE0F7D61240040F377 /* sharedbraycurtis.cpp in Sources */,
375873AF0F7D61240040F377 /* sharedkulczynski.cpp in Sources */,
375873B00F7D61240040F377 /* sharedkulczynskicody.cpp in Sources */,
375873B10F7D61240040F377 /* sharedlennon.cpp in Sources */,
375873B20F7D61240040F377 /* sharedmorisitahorn.cpp in Sources */,
375873B30F7D61240040F377 /* sharedochiai.cpp in Sources */,
- 375873E30F7D63B50040F377 /* sharedanderberg.cpp in Sources */,
375873E70F7D63E90040F377 /* coverage.cpp in Sources */,
375873EC0F7D64520040F377 /* fullmatrix.cpp in Sources */,
375873EF0F7D646F0040F377 /* heatmap.cpp in Sources */,
#include "sharedbdiversity.h"
#include "sharednseqs.h"
#include "sharedochiai.h"
-#include "sharedanderberg.h"
+//#include "sharedanderberg.h"
#include "sharedkulczynski.h"
#include "sharedkulczynskicody.h"
#include "sharedlennon.h"
cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs")));
}else if (globaldata->Estimators[i] == "sharedochiai") {
cDisplays.push_back(new CollectDisplay(new SharedOchiai(), new SharedOneColumnFile(fileNameRoot+"shared.ochiai")));
- }else if (globaldata->Estimators[i] == "sharedanderberg") {
- cDisplays.push_back(new CollectDisplay(new SharedAnderberg(), new SharedOneColumnFile(fileNameRoot+"shared.anderberg")));
+ //}else if (globaldata->Estimators[i] == "sharedanderberg") {
+ // cDisplays.push_back(new CollectDisplay(new SharedAnderberg(), new SharedOneColumnFile(fileNameRoot+"shared.anderberg")));
}else if (globaldata->Estimators[i] == "sharedkulczynski") {
cDisplays.push_back(new CollectDisplay(new SharedKulczynski(), new SharedOneColumnFile(fileNameRoot+"shared.kulczynski")));
}else if (globaldata->Estimators[i] == "sharedkulczynskicody") {
+++ /dev/null
-/*
- * sharedanderberg.cpp
- * Mothur
- *
- * Created by Sarah Westcott on 3/23/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "sharedanderberg.h"
-
-/***********************************************************************/
-
-EstOutput SharedAnderberg::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
- try {
- int S1, S2, S12, tempA, tempB;
- S1 = 0; S2 = 0; S12 = 0; tempA = 0; tempB = 0;
-
- /*S1, S2 = number of OTUs observed or estimated in A and B
- S12=number of OTUs shared between A and B */
-
- data.resize(1,0);
-
- for (int i = 0; i < shared1->size(); i++) {
- //store in temps to avoid multiple repetitive function calls
- tempA = shared1->getAbundance(i);
- tempB = shared2->getAbundance(i);
-
- if (tempA != 0) { S1++; }
- if (tempB != 0) { S2++; }
-
- //they are shared
- if ((tempA != 0) && (tempB != 0)) { S12++; }
- }
-
- data[0] = S12 / ((float)((2 * S1) + (2 * S2) - (3 * S12)));
-
- if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
-
- return data;
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedAnderberg class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedAnderberg class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-
-/***********************************************************************/