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Merges 1.38.0 into opticluster branch

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1 parent a591ad7 commit 6c5ebe51b6b2b49e31a14c9eb9da2e38fbde0930 @mothur-westcott mothur-westcott committed Jun 30, 2016
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30 Mothur.xcodeproj/project.pbxproj
@@ -387,8 +387,11 @@
4888416D1CC7F1B900C5E972 /* optimatrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 4888416B1CC7F1B900C5E972 /* optimatrix.cpp */; };
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4893DE2918EEF28100C615DF /* (null) in Sources */ = {isa = PBXBuildFile; };
+ 48A11C6E1CDA40F0003481D8 /* testrenamefilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48A11C6C1CDA40F0003481D8 /* testrenamefilecommand.cpp */; };
48A85BAD18E1AF2000199B6F /* (null) in Sources */ = {isa = PBXBuildFile; };
48B662031BBB1B6600997EE4 /* testrenameseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48B662011BBB1B6600997EE4 /* testrenameseqscommand.cpp */; };
+ 48C1DDC61D25C1BC00B5BA9D /* distcdataset.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48C1DDC21D25C1BC00B5BA9D /* distcdataset.cpp */; };
+ 48C1DDC71D25C1BC00B5BA9D /* testopticluster.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48C1DDC41D25C1BC00B5BA9D /* testopticluster.cpp */; };
48C51DF01A76B888004ECDF1 /* fastqread.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48C51DEF1A76B888004ECDF1 /* fastqread.cpp */; };
48C51DF31A793EFE004ECDF1 /* kmeralign.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48C51DF11A793EFE004ECDF1 /* kmeralign.cpp */; };
48C728651B66A77800D40830 /* testsequence.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48C728641B66A77800D40830 /* testsequence.cpp */; };
@@ -402,9 +405,9 @@
48D6E96B1CA4262A008DF76B /* dataset.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48D6E9691CA4262A008DF76B /* dataset.cpp */; };
48DB37B31B3B27E000C372A4 /* makefilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48DB37B11B3B27E000C372A4 /* makefilecommand.cpp */; };
48DB37B41B3B27E000C372A4 /* makefilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48DB37B11B3B27E000C372A4 /* makefilecommand.cpp */; };
- 48E418561D08893A004C36AB /* distcdataset.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48E418541D08893A004C36AB /* distcdataset.cpp */; };
+ 48E418561D08893A004C36AB /* (null) in Sources */ = {isa = PBXBuildFile; };
48E981CF189C38FB0042BE9D /* (null) in Sources */ = {isa = PBXBuildFile; };
- 48EDB7691D11DBAF00F76E93 /* testopticluster.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48EDB7671D11DBAF00F76E93 /* testopticluster.cpp */; };
+ 48EDB76C1D1320DD00F76E93 /* chimeravsearchcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48EDB76A1D1320DD00F76E93 /* chimeravsearchcommand.cpp */; };
48F98E4D1A9CFD670005E81B /* completelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48F98E4C1A9CFD670005E81B /* completelinkage.cpp */; };
7E6BE10A12F710D8007ADDBE /* refchimeratest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */; };
834D9D581656D7C400E7FAB9 /* regularizedrandomforest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 834D9D561656D7C400E7FAB9 /* regularizedrandomforest.cpp */; };
@@ -842,6 +845,10 @@
48A11C6D1CDA40F0003481D8 /* testrenamefilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = testrenamefilecommand.h; path = testcommands/testrenamefilecommand.h; sourceTree = "<group>"; };
48B662011BBB1B6600997EE4 /* testrenameseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = testrenameseqscommand.cpp; path = testcommands/testrenameseqscommand.cpp; sourceTree = "<group>"; };
48B662021BBB1B6600997EE4 /* testrenameseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = testrenameseqscommand.h; path = testcommands/testrenameseqscommand.h; sourceTree = "<group>"; };
+ 48C1DDC21D25C1BC00B5BA9D /* distcdataset.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distcdataset.cpp; sourceTree = "<group>"; };
+ 48C1DDC31D25C1BC00B5BA9D /* distcdataset.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = distcdataset.h; sourceTree = "<group>"; };
+ 48C1DDC41D25C1BC00B5BA9D /* testopticluster.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = testopticluster.cpp; sourceTree = "<group>"; };
+ 48C1DDC51D25C1BC00B5BA9D /* testopticluster.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = testopticluster.h; sourceTree = "<group>"; };
48C51DEE1A76B870004ECDF1 /* fastqread.h */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.c.h; name = fastqread.h; path = source/datastructures/fastqread.h; sourceTree = SOURCE_ROOT; };
48C51DEF1A76B888004ECDF1 /* fastqread.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = fastqread.cpp; path = source/datastructures/fastqread.cpp; sourceTree = SOURCE_ROOT; };
48C51DF11A793EFE004ECDF1 /* kmeralign.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = kmeralign.cpp; path = source/datastructures/kmeralign.cpp; sourceTree = SOURCE_ROOT; };
@@ -862,10 +869,8 @@
48D6E96A1CA4262A008DF76B /* dataset.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dataset.h; sourceTree = "<group>"; };
48DB37B11B3B27E000C372A4 /* makefilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = makefilecommand.cpp; path = source/commands/makefilecommand.cpp; sourceTree = SOURCE_ROOT; };
48DB37B21B3B27E000C372A4 /* makefilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = makefilecommand.h; path = source/commands/makefilecommand.h; sourceTree = SOURCE_ROOT; };
- 48E418541D08893A004C36AB /* distcdataset.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distcdataset.cpp; sourceTree = "<group>"; };
- 48E418551D08893A004C36AB /* distcdataset.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = distcdataset.h; sourceTree = "<group>"; };
- 48EDB7671D11DBAF00F76E93 /* testopticluster.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = testopticluster.cpp; sourceTree = "<group>"; };
- 48EDB7681D11DBAF00F76E93 /* testopticluster.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = testopticluster.h; sourceTree = "<group>"; };
+ 48EDB76A1D1320DD00F76E93 /* chimeravsearchcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = chimeravsearchcommand.cpp; path = source/commands/chimeravsearchcommand.cpp; sourceTree = "<group>"; };
+ 48EDB76B1D1320DD00F76E93 /* chimeravsearchcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = chimeravsearchcommand.h; path = source/commands/chimeravsearchcommand.h; sourceTree = "<group>"; };
48F98E4C1A9CFD670005E81B /* completelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = completelinkage.cpp; path = source/completelinkage.cpp; sourceTree = SOURCE_ROOT; };
7B2181FE17AD777B00286E6A /* classifysvmsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = classifysvmsharedcommand.cpp; path = source/commands/classifysvmsharedcommand.cpp; sourceTree = SOURCE_ROOT; };
7B2181FF17AD777B00286E6A /* classifysvmsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = classifysvmsharedcommand.h; path = source/commands/classifysvmsharedcommand.h; sourceTree = SOURCE_ROOT; };
@@ -1737,14 +1742,14 @@
481FB51B1AC0A63E0076CFF3 /* main.cpp */,
48D6E9691CA4262A008DF76B /* dataset.cpp */,
48D6E96A1CA4262A008DF76B /* dataset.h */,
- 48E418541D08893A004C36AB /* distcdataset.cpp */,
- 48E418551D08893A004C36AB /* distcdataset.h */,
48576EA61D05F59300BBC9C0 /* distpdataset.cpp */,
48576EA71D05F59300BBC9C0 /* distpdataset.h */,
+ 48C1DDC21D25C1BC00B5BA9D /* distcdataset.cpp */,
+ 48C1DDC31D25C1BC00B5BA9D /* distcdataset.h */,
4827A4DA1CB3ED2100345170 /* fastqdataset.cpp */,
4827A4DB1CB3ED2100345170 /* fastqdataset.h */,
- 48EDB7671D11DBAF00F76E93 /* testopticluster.cpp */,
- 48EDB7681D11DBAF00F76E93 /* testopticluster.h */,
+ 48C1DDC41D25C1BC00B5BA9D /* testopticluster.cpp */,
+ 48C1DDC51D25C1BC00B5BA9D /* testopticluster.h */,
48D6E9661CA42389008DF76B /* testvsearchfileparser.cpp */,
48D6E9671CA42389008DF76B /* testvsearchfileparser.h */,
481FB5221AC0AA010076CFF3 /* testcontainers */,
@@ -2615,7 +2620,6 @@
481FB64E1AC1B7F40076CFF3 /* treenode.cpp in Sources */,
481FB5801AC1B6EA0076CFF3 /* weighted.cpp in Sources */,
481FB54F1AC1B63A0076CFF3 /* memeuclidean.cpp in Sources */,
- 48EDB7691D11DBAF00F76E93 /* testopticluster.cpp in Sources */,
481FB5611AC1B69B0076CFF3 /* sharedjsd.cpp in Sources */,
481FB5AF1AC1B7300076CFF3 /* createdatabasecommand.cpp in Sources */,
481FB5731AC1B6EA0076CFF3 /* simpsoneven.cpp in Sources */,
@@ -2760,6 +2764,7 @@
481FB6811AC1B8960076CFF3 /* subsample.cpp in Sources */,
481FB5521AC1B6450076CFF3 /* odum.cpp in Sources */,
481FB68E1AC1BA9E0076CFF3 /* kmernode.cpp in Sources */,
+ 48C1DDC71D25C1BC00B5BA9D /* testopticluster.cpp in Sources */,
481FB5CE1AC1B75C0076CFF3 /* homovacommand.cpp in Sources */,
481FB6551AC1B8100076CFF3 /* heatmap.cpp in Sources */,
481FB5E61AC1B77E0076CFF3 /* normalizesharedcommand.cpp in Sources */,
@@ -2821,6 +2826,7 @@
481FB63B1AC1B7EA0076CFF3 /* rabundvector.cpp in Sources */,
481FB5A91AC1B7300076CFF3 /* collectsharedcommand.cpp in Sources */,
481FB6211AC1B7BA0076CFF3 /* communitytype.cpp in Sources */,
+ 48C1DDC61D25C1BC00B5BA9D /* distcdataset.cpp in Sources */,
481FB5621AC1B69E0076CFF3 /* sharedkstest.cpp in Sources */,
481FB5E91AC1B77E0076CFF3 /* otuhierarchycommand.cpp in Sources */,
481FB5351AC1B5D90076CFF3 /* fasta.cpp in Sources */,
@@ -2933,7 +2939,7 @@
481FB5C21AC1B74F0076CFF3 /* getoturepcommand.cpp in Sources */,
481FB5D01AC1B75C0076CFF3 /* kruskalwalliscommand.cpp in Sources */,
48B662031BBB1B6600997EE4 /* testrenameseqscommand.cpp in Sources */,
- 48E418561D08893A004C36AB /* distcdataset.cpp in Sources */,
+ 48E418561D08893A004C36AB /* (null) in Sources */,
481FB5511AC1B6410076CFF3 /* npshannon.cpp in Sources */,
481FB6471AC1B7EA0076CFF3 /* sparsematrix.cpp in Sources */,
481FB5871AC1B6FF0076CFF3 /* decalc.cpp in Sources */,
View
1 source/cluster.hpp
@@ -5,6 +5,7 @@
#include "optimatrix.h"
#include "mothurout.h"
#include "rabundvector.hpp"
+#include "listvector.hpp"
class ListVector;
View
24 source/commands/clustersplitcommand.cpp
@@ -661,22 +661,22 @@ map<double, int> ClusterSplitCommand::completeListFile(vector<string> listNames,
numSingleBins = listSingle->getNumBins();
}else{ listSingle = NULL; numSingleBins = 0; }
-
- //go through users set and make them floats so we can sort them
+
+ //go through users set and make them floats so we can sort them
double tcutoff = cutoff * 1000; tcutoff = ceil(tcutoff);
- for(set<string>::iterator it = userLabels.begin(); it != userLabels.end(); ++it) {
- double temp = -10.0;
-
- if ((*it != "unique") && (convertTestFloat(*it, temp) == true)) { m->mothurConvert(*it, temp); }
- else if (*it == "unique") { temp = -1.0; }
+ for(set<string>::iterator it = userLabels.begin(); it != userLabels.end(); ++it) {
+ double temp = -10.0;
+
+ if ((*it != "unique") && (convertTestFloat(*it, temp) == true)) { m->mothurConvert(*it, temp); }
+ else if (*it == "unique") { temp = -1.0; }
double ttemp = temp * 1000; ttemp = ceil(temp);
- if (ttemp <= tcutoff) {
- orderFloat.push_back(temp);
- labelBin[temp] = numSingleBins; //initialize numbins
- }
- }
+ if (ttemp <= tcutoff) {
+ orderFloat.push_back(temp);
+ labelBin[temp] = numSingleBins; //initialize numbins
+ }
+ }
//sort order
sort(orderFloat.begin(), orderFloat.end());
View
9 source/commands/makecontigscommand.cpp
@@ -3292,13 +3292,8 @@ bool MakeContigsCommand::fixName(string& forward){
if (nameType == poundMatch) {
match = true;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- forward = (forward.substr(0, poundMatchPos));
- }else { //it does not match
- int pos = forward.find_last_of('#');
- if (pos != string::npos) { forward = forward.substr(0, pos); }
- }
+ int pos = forward.find_last_of('#');
+ if (pos != string::npos) { forward = forward.substr(0, pos); }
}else if (nameType == perfectMatch) { match = true; }
return match;

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