Added get.line command.

Added get.label command.
Added get.group command.
Added parameter and parameter value error checking.
Modified ace to allow changing the abund variable.
Made it so you don't need a space after the comma when entering parameters.
Added error checking for invalid labels.
Added a new convert method that tests if a given string can be converted into an int.

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 93e0e58cf60e16ef5098d680acc14637f59403c0..d3716c77281a1535db35ac892336f89d66694654 100644 (file)
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+               37D928520F21331F001D4494 /* validcommands.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validcommands.h; sourceTree = SOURCE_ROOT; };
+               37D928530F21331F001D4494 /* validparameter.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validparameter.cpp; sourceTree = SOURCE_ROOT; };
+               37D928540F21331F001D4494 /* validparameter.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validparameter.h; sourceTree = SOURCE_ROOT; };
+               37E5F3E10F29FD4200F8D827 /* treenode.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treenode.h; sourceTree = SOURCE_ROOT; };
+               37E5F3E20F29FD4200F8D827 /* treenode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treenode.cpp; sourceTree = SOURCE_ROOT; };
+               37E5F4900F2A3DA800F8D827 /* readtreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtreecommand.h; sourceTree = SOURCE_ROOT; };
+               37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtreecommand.cpp; sourceTree = SOURCE_ROOT; };
+               7E44EBD00F32358B00B0D45D /* makefile */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.make; path = makefile; sourceTree = "<group>"; };

                8DD76F6C0486A84900D96B5E /* mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = mothur; sourceTree = BUILT_PRODUCTS_DIR; };
                C6859E8B029090EE04C91782 /* Mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = Mothur.1; sourceTree = "<group>"; };
                8DD76F6C0486A84900D96B5E /* mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = mothur; sourceTree = BUILT_PRODUCTS_DIR; };
                C6859E8B029090EE04C91782 /* Mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = Mothur.1; sourceTree = "<group>"; };

+               EBA52D2A0F378B0F00122C15 /* getgroupcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getgroupcommand.h; sourceTree = "<group>"; };
+               EBA52D2B0F378B0F00122C15 /* getgroupcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getgroupcommand.cpp; sourceTree = "<group>"; };
+               EBFD67820F33876C00883537 /* getlabelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlabelcommand.h; sourceTree = "<group>"; };
+               EBFD67830F33876C00883537 /* getlabelcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlabelcommand.cpp; sourceTree = "<group>"; };
+               EBFD67E60F339AAA00883537 /* getlinecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlinecommand.h; sourceTree = "<group>"; };
+               EBFD67E70F339AAA00883537 /* getlinecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlinecommand.cpp; sourceTree = "<group>"; };

 /* End PBXFileReference section */
 
 /* Begin PBXFrameworksBuildPhase section */
 /* End PBXFileReference section */
 
 /* Begin PBXFrameworksBuildPhase section */


@@ -338,6 +324,7 @@
                                37D927D60F21331F001D4494 /* display.h */,
                                37D927D80F21331F001D4494 /* engine.hpp */,
                                37D927D70F21331F001D4494 /* engine.cpp */,
                                37D927D60F21331F001D4494 /* display.h */,
                                37D927D80F21331F001D4494 /* engine.hpp */,
                                37D927D70F21331F001D4494 /* engine.cpp */,

+                               7E44EBD00F32358B00B0D45D /* makefile */,

                                37D928B10F213472001D4494 /* errorcheckor */,
                                37D927DE0F21331F001D4494 /* fileoutput.h */,
                                37D927DD0F21331F001D4494 /* fileoutput.cpp */,
                                37D928B10F213472001D4494 /* errorcheckor */,
                                37D927DE0F21331F001D4494 /* fileoutput.h */,
                                37D927DD0F21331F001D4494 /* fileoutput.cpp */,


@@ -376,7 +363,7 @@
                                37D9284C0F21331F001D4494 /* utilities.hpp */,
                        );
                        name = Source;
                                37D9284C0F21331F001D4494 /* utilities.hpp */,
                        );
                        name = Source;

-                       sourceTree = "<group>";
+                       sourceTree = SOURCE_ROOT;

                };
                1AB674ADFE9D54B511CA2CBB /* Products */ = {
                        isa = PBXGroup;
                };
                1AB674ADFE9D54B511CA2CBB /* Products */ = {
                        isa = PBXGroup;


@@ -390,7 +377,6 @@
                        isa = PBXGroup;
                        children = (
                                37D927BE0F21331F001D4494 /* calculator.h */,
                        isa = PBXGroup;
                        children = (
                                37D927BE0F21331F001D4494 /* calculator.h */,

-                               3792948D0F2E271100B9034A /* treecalculator.h */,

                                37D927BD0F21331F001D4494 /* calculator.cpp */,
                                37D927B90F21331F001D4494 /* ace.h */,
                                37D927B80F21331F001D4494 /* ace.cpp */,
                                37D927BD0F21331F001D4494 /* calculator.cpp */,
                                37D927B90F21331F001D4494 /* ace.h */,
                                37D927B80F21331F001D4494 /* ace.cpp */,


@@ -402,8 +388,6 @@
                                37D927E70F21331F001D4494 /* jackknife.cpp */,
                                37D927F50F21331F001D4494 /* npshannon.h */,
                                37D927F40F21331F001D4494 /* npshannon.cpp */,
                                37D927E70F21331F001D4494 /* jackknife.cpp */,
                                37D927F50F21331F001D4494 /* npshannon.h */,
                                37D927F40F21331F001D4494 /* npshannon.cpp */,

-                               379294880F2E258500B9034A /* parsimony.h */,
-                               379294890F2E258500B9034A /* parsimony.cpp */,

                                37D928020F21331F001D4494 /* rarecalc.h */,
                                37D928010F21331F001D4494 /* rarecalc.cpp */,
                                37D9281F0F21331F001D4494 /* shannon.h */,
                                37D928020F21331F001D4494 /* rarecalc.h */,
                                37D928010F21331F001D4494 /* rarecalc.cpp */,
                                37D9281F0F21331F001D4494 /* shannon.h */,


@@ -420,8 +404,6 @@
                                37D9282C0F21331F001D4494 /* sharedjest.cpp */,
                                37D928350F21331F001D4494 /* sharedsobs.h */,
                                37D928340F21331F001D4494 /* sharedsobs.cpp */,
                                37D9282C0F21331F001D4494 /* sharedjest.cpp */,
                                37D928350F21331F001D4494 /* sharedsobs.h */,
                                37D928340F21331F001D4494 /* sharedsobs.cpp */,

-                               37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */,
-                               37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */,

                                37D928370F21331F001D4494 /* sharedsorabund.h */,
                                37D928360F21331F001D4494 /* sharedsorabund.cpp */,
                                37D928390F21331F001D4494 /* sharedsorclass.h */,
                                37D928370F21331F001D4494 /* sharedsorabund.h */,
                                37D928360F21331F001D4494 /* sharedsorabund.cpp */,
                                37D928390F21331F001D4494 /* sharedsorclass.h */,


@@ -435,15 +417,11 @@
                                37D928410F21331F001D4494 /* simpson.h */,
                                37D928400F21331F001D4494 /* simpson.cpp */,
                                37D928430F21331F001D4494 /* sobs.h */,
                                37D928410F21331F001D4494 /* simpson.h */,
                                37D928400F21331F001D4494 /* simpson.cpp */,
                                37D928430F21331F001D4494 /* sobs.h */,

-                               374610810F40652400460C57 /* unweighted.h */,
-                               374610820F40652400460C57 /* unweighted.cpp */,

                                37D9284E0F21331F001D4494 /* uvest.h */,
                                37D9284D0F21331F001D4494 /* uvest.cpp */,
                                37D9284E0F21331F001D4494 /* uvest.h */,
                                37D9284D0F21331F001D4494 /* uvest.cpp */,

-                               3746107C0F4064D100460C57 /* weighted.h */,
-                               3746107D0F4064D100460C57 /* weighted.cpp */,

                        );
                        name = calculators;
                        );
                        name = calculators;

-                       sourceTree = "<group>";
+                       sourceTree = SOURCE_ROOT;

                };
                37D928A90F2133E5001D4494 /* commands */ = {
                        isa = PBXGroup;
                };
                37D928A90F2133E5001D4494 /* commands */ = {
                        isa = PBXGroup;


@@ -457,16 +435,18 @@
                                37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */,
                                37B28F660F27590100808A62 /* deconvolutecommand.h */,
                                37B28F670F27590100808A62 /* deconvolutecommand.cpp */,
                                37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */,
                                37B28F660F27590100808A62 /* deconvolutecommand.h */,
                                37B28F670F27590100808A62 /* deconvolutecommand.cpp */,

+                               EBA52D2A0F378B0F00122C15 /* getgroupcommand.h */,
+                               EBA52D2B0F378B0F00122C15 /* getgroupcommand.cpp */,
+                               EBFD67820F33876C00883537 /* getlabelcommand.h */,
+                               EBFD67830F33876C00883537 /* getlabelcommand.cpp */,
+                               EBFD67E60F339AAA00883537 /* getlinecommand.h */,
+                               EBFD67E70F339AAA00883537 /* getlinecommand.cpp */,

                                37D927E40F21331F001D4494 /* helpcommand.h */,
                                37D927E30F21331F001D4494 /* helpcommand.cpp */,
                                37D927F20F21331F001D4494 /* nocommand.cpp */,
                                37D927F30F21331F001D4494 /* nocommand.h */,
                                37D927FA0F21331F001D4494 /* parselistcommand.h */,
                                37D927F90F21331F001D4494 /* parselistcommand.cpp */,
                                37D927E40F21331F001D4494 /* helpcommand.h */,
                                37D927E30F21331F001D4494 /* helpcommand.cpp */,
                                37D927F20F21331F001D4494 /* nocommand.cpp */,
                                37D927F30F21331F001D4494 /* nocommand.h */,
                                37D927FA0F21331F001D4494 /* parselistcommand.h */,
                                37D927F90F21331F001D4494 /* parselistcommand.cpp */,

-                               3792946E0F2E191800B9034A /* parsimonycommand.h */,
-                               3792946F0F2E191800B9034A /* parsimonycommand.cpp */,
-                               37D927FE0F21331F001D4494 /* quitcommand.h */,
-                               37D927FD0F21331F001D4494 /* quitcommand.cpp */,

                                37D928080F21331F001D4494 /* rarefactcommand.h */,
                                37D928070F21331F001D4494 /* rarefactcommand.cpp */,
                                37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */,
                                37D928080F21331F001D4494 /* rarefactcommand.h */,
                                37D928070F21331F001D4494 /* rarefactcommand.cpp */,
                                37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */,


@@ -475,8 +455,6 @@
                                372E12950F263D5A0095CF7E /* readdistcommand.cpp */,
                                372E126E0F26365B0095CF7E /* readotucommand.h */,
                                372E126F0F26365B0095CF7E /* readotucommand.cpp */,
                                372E12950F263D5A0095CF7E /* readdistcommand.cpp */,
                                372E126E0F26365B0095CF7E /* readotucommand.h */,
                                372E126F0F26365B0095CF7E /* readotucommand.cpp */,

-                               37AFC7A10F44703E005F492D /* readsharedcommand.h */,
-                               37AFC7A20F44703E005F492D /* readsharedcommand.cpp */,

                                37E5F4900F2A3DA800F8D827 /* readtreecommand.h */,
                                37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */,
                                37D928270F21331F001D4494 /* sharedcommand.h */,
                                37E5F4900F2A3DA800F8D827 /* readtreecommand.h */,
                                37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */,
                                37D928270F21331F001D4494 /* sharedcommand.h */,


@@ -485,13 +463,11 @@
                                37D928460F21331F001D4494 /* summarycommand.cpp */,
                                37D9284B0F21331F001D4494 /* summarysharedcommand.h */,
                                37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */,
                                37D928460F21331F001D4494 /* summarycommand.cpp */,
                                37D9284B0F21331F001D4494 /* summarysharedcommand.h */,
                                37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */,

-                               3746109B0F40657600460C57 /* unifracunweightedcommand.h */,
-                               3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */,
-                               374610760F40645300460C57 /* unifracweightedcommand.h */,
-                               374610770F40645300460C57 /* unifracweightedcommand.cpp */,
+                               37D927FE0F21331F001D4494 /* quitcommand.h */,
+                               37D927FD0F21331F001D4494 /* quitcommand.cpp */,

                        );
                        name = commands;
                        );
                        name = commands;

-                       sourceTree = "<group>";
+                       sourceTree = SOURCE_ROOT;

                };
                37D928AC0F213420001D4494 /* containers */ = {
                        isa = PBXGroup;
                };
                37D928AC0F213420001D4494 /* containers */ = {
                        isa = PBXGroup;


@@ -525,7 +501,7 @@
                                37E5F3E20F29FD4200F8D827 /* treenode.cpp */,
                        );
                        name = containers;
                                37E5F3E20F29FD4200F8D827 /* treenode.cpp */,
                        );
                        name = containers;

-                       sourceTree = "<group>";
+                       sourceTree = SOURCE_ROOT;

                };
                37D928B10F213472001D4494 /* errorcheckor */ = {
                        isa = PBXGroup;
                };
                37D928B10F213472001D4494 /* errorcheckor */ = {
                        isa = PBXGroup;


@@ -540,7 +516,7 @@
                                37D928530F21331F001D4494 /* validparameter.cpp */,
                        );
                        name = errorcheckor;
                                37D928530F21331F001D4494 /* validparameter.cpp */,
                        );
                        name = errorcheckor;

-                       sourceTree = "<group>";
+                       sourceTree = SOURCE_ROOT;

                };
                C6859E8C029090F304C91782 /* Documentation */ = {
                        isa = PBXGroup;
                };
                C6859E8C029090F304C91782 /* Documentation */ = {
                        isa = PBXGroup;


@@ -671,14 +647,10 @@
                                37E5F3E30F29FD4200F8D827 /* treenode.cpp in Sources */,
                                37E5F4920F2A3DA800F8D827 /* readtreecommand.cpp in Sources */,
                                379293C30F2DE73400B9034A /* treemap.cpp in Sources */,
                                37E5F3E30F29FD4200F8D827 /* treenode.cpp in Sources */,
                                37E5F4920F2A3DA800F8D827 /* readtreecommand.cpp in Sources */,
                                379293C30F2DE73400B9034A /* treemap.cpp in Sources */,

-                               379294700F2E191800B9034A /* parsimonycommand.cpp in Sources */,
-                               3792948A0F2E258500B9034A /* parsimony.cpp in Sources */,
-                               374610780F40645300460C57 /* unifracweightedcommand.cpp in Sources */,
-                               3746107E0F4064D100460C57 /* weighted.cpp in Sources */,
-                               374610830F40652400460C57 /* unweighted.cpp in Sources */,
-                               3746109D0F40657600460C57 /* unifracunweightedcommand.cpp in Sources */,
-                               37AFC71F0F445386005F492D /* sharedsobscollectsummary.cpp in Sources */,
-                               37AFC7A30F44703E005F492D /* readsharedcommand.cpp in Sources */,
+                               7E44EBD10F3235D900B0D45D /* makefile in Sources */,
+                               EBFD67840F33876C00883537 /* getlabelcommand.cpp in Sources */,
+                               EBFD67E80F339AAA00883537 /* getlinecommand.cpp in Sources */,
+                               EBA52D2C0F378B0F00122C15 /* getgroupcommand.cpp in Sources */,

                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };


@@ -692,7 +664,7 @@
                                GCC_DYNAMIC_NO_PIC = NO;
                                GCC_ENABLE_FIX_AND_CONTINUE = YES;
                                GCC_MODEL_TUNING = G5;
                                GCC_DYNAMIC_NO_PIC = NO;
                                GCC_ENABLE_FIX_AND_CONTINUE = YES;
                                GCC_MODEL_TUNING = G5;

-                               GCC_OPTIMIZATION_LEVEL = 3;
+                               GCC_OPTIMIZATION_LEVEL = 0;

                                GCC_PREPROCESSOR_DEFINITIONS = (
                                        "_GLIBCXX_DEBUG=1",
                                        "_GLIBCXX_DEBUG_PEDANTIC=1",
                                GCC_PREPROCESSOR_DEFINITIONS = (
                                        "_GLIBCXX_DEBUG=1",
                                        "_GLIBCXX_DEBUG_PEDANTIC=1",


@@ -708,7 +680,6 @@
                        buildSettings = {
                                DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
                                GCC_MODEL_TUNING = G5;
                        buildSettings = {
                                DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
                                GCC_MODEL_TUNING = G5;

-                               GCC_OPTIMIZATION_LEVEL = 3;

                                INSTALL_PATH = /usr/local/bin;
                                PRODUCT_NAME = mothur;
                        };
                                INSTALL_PATH = /usr/local/bin;
                                PRODUCT_NAME = mothur;
                        };


@@ -732,7 +703,7 @@
                                        ppc,
                                        i386,
                                );
                                        ppc,
                                        i386,
                                );

-                               GCC_OPTIMIZATION_LEVEL = 0;
+                               GCC_OPTIMIZATION_LEVEL = 3;

                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
                                PREBINDING = NO;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
                                PREBINDING = NO;

diff --git a/ace.cpp b/ace.cpp
index 064779467d92c14a514f9ad10c4fd714763401ed..d074310ab1678ca44abbb23372ee74b41321999b 100644 (file)
--- a/ace.cpp
+++ b/ace.cpp
@@ -13,6 +13,7 @@
 
 EstOutput Ace::getValues(SAbundVector* rank) {
        try {
 
 EstOutput Ace::getValues(SAbundVector* rank) {
        try {

+               cout << "abund = " << abund << "\n";

                data.resize(3,0);
        //      vector<double> aceData(3,0);
                double ace, acelci, acehci;
                data.resize(3,0);
        //      vector<double> aceData(3,0);
                double ace, acelci, acehci;

diff --git a/ace.h b/ace.h
index 4c4a69de67c1b4ccccf9aa0d4adc33927b2fd6c2..b81dd64eef6c0cd24d354416f0dd6e3583b83bd2 100644 (file)
--- a/ace.h
+++ b/ace.h
@@ -20,7 +20,7 @@ It is a child of the calculator class. */
 class Ace : public Calculator  {
        
 public:
 class Ace : public Calculator  {
        
 public:

-       Ace(int n=10) : abund(n), Calculator("ACE", 3) {};
+       Ace(int n) : abund(n), Calculator("ACE", 3) {};

        EstOutput getValues(SAbundVector*);
        EstOutput getValues(SharedRAbundVector*, SharedRAbundVector*) {return data;};
 private:
        EstOutput getValues(SAbundVector*);
        EstOutput getValues(SharedRAbundVector*, SharedRAbundVector*) {return data;};
 private:

diff --git a/collect.cpp b/collect.cpp
index 2ed5ca7f10eeefdb860ae9fc7b5859b5eb239c0e..1c8128aef4ba42ec11fc2a7edbaa8cd42aa97ced 100644 (file)
--- a/collect.cpp
+++ b/collect.cpp
@@ -64,7 +64,8 @@ void Collect::getSharedCurve(int increment = 1){
 try {
                globaldata = GlobalData::getInstance();
                vector<SharedRAbundVector*> lookup; 
 try {
                globaldata = GlobalData::getInstance();
                vector<SharedRAbundVector*> lookup; 

-
+               vector<string> chosenGroups = globaldata->sharedGroups;
+               

                //create and initialize vector of sharedvectors, one for each group
                for (int i = 0; i < globaldata->gGroupmap->getNumGroups(); i++) { 
                        SharedRAbundVector* temp = new SharedRAbundVector(sharedorder->getNumBins());
                //create and initialize vector of sharedvectors, one for each group
                for (int i = 0; i < globaldata->gGroupmap->getNumGroups(); i++) { 
                        SharedRAbundVector* temp = new SharedRAbundVector(sharedorder->getNumBins());


@@ -78,7 +79,7 @@ try {
        
                //initialize labels for output
                //makes  'uniqueAB       uniqueAC  uniqueBC' if your groups are A, B, C
        
                //initialize labels for output
                //makes  'uniqueAB       uniqueAC  uniqueBC' if your groups are A, B, C

-               getGroupComb();
+               getGroupComb(chosenGroups);

                groupLabel = "";
                for (int s = 0; s < groupComb.size(); s++) {
                        groupLabel = groupLabel + label + groupComb[s] + "\t";
                groupLabel = "";
                for (int s = 0; s < groupComb.size(); s++) {
                        groupLabel = groupLabel + label + groupComb[s] + "\t";


@@ -94,7 +95,6 @@ try {
                        //get first sample
                        individual chosen = sharedorder->get(i);
                        int abundance; 
                        //get first sample
                        individual chosen = sharedorder->get(i);
                        int abundance; 

-                                       

                        //set info for sharedvector in chosens group
                        for (int j = 0; j < lookup.size(); j++) { 
                                if (chosen.group == lookup[j]->getGroup()) {
                        //set info for sharedvector in chosens group
                        for (int j = 0; j < lookup.size(); j++) { 
                                if (chosen.group == lookup[j]->getGroup()) {


@@ -103,7 +103,7 @@ try {
                                         break;
                                }
                        }
                                         break;
                                }
                        }

-                       
+

                        //calculate at 0 and the given increment
                        if((i == 0) || (i+1) % increment == 0){
                                //randomize group order
                        //calculate at 0 and the given increment
                        if((i == 0) || (i+1) % increment == 0){
                                //randomize group order


@@ -116,8 +116,8 @@ try {
                                        }
                                        n++;
                                }
                                        }
                                        n++;
                                }

-                       }

                        totalNumSeq = i+1;
                        totalNumSeq = i+1;

+                       }

                }
                
                //calculate last line if you haven't already
                }
                
                //calculate last line if you haven't already


@@ -150,7 +150,7 @@ try {
 
 /**************************************************************************************/
 
 
 /**************************************************************************************/
 

-void Collect::getGroupComb() {
+void Collect::getGroupComb(vector<string> chosen) {

                string group;
                
                numGroupComb = 0;
                string group;
                
                numGroupComb = 0;


@@ -158,13 +158,28 @@ void Collect::getGroupComb() {
                int n = 1;
                for (int i = 0; i < (globaldata->gGroupmap->getNumGroups() - 1); i++) {
                        for (int l = n; l < globaldata->gGroupmap->getNumGroups(); l++) {
                int n = 1;
                for (int i = 0; i < (globaldata->gGroupmap->getNumGroups() - 1); i++) {
                        for (int l = n; l < globaldata->gGroupmap->getNumGroups(); l++) {

-                               group = globaldata->gGroupmap->namesOfGroups[i] + globaldata->gGroupmap->namesOfGroups[l];
-                               groupComb.push_back(group);     
-                               numGroupComb++;
+                               string g1 = globaldata->gGroupmap->namesOfGroups[i];
+                               string g2 = globaldata->gGroupmap->namesOfGroups[l];
+                               if(validGroup(chosen, g1) && validGroup(chosen, g2)) { 
+                                       group = g1 + g2;
+                                       groupComb.push_back(group);     
+                                       numGroupComb++;
+                               }

                        }
                        n++;
                }
                        }
                        n++;
                }

-

 }
 
 /**************************************************************************************/
 }
 
 /**************************************************************************************/

+
+bool Collect::validGroup(vector<string> chosen, string group) {
+       if(chosen.size() == 0)
+               return true;
+       for(int i = 0; i < chosen.size(); i++)
+               if(chosen.at(i).compare(group) == 0)
+                       return true;
+       return false;
+}
+                                       
+
+

diff --git a/collect.h b/collect.h
index fe78dda86f6088f7395f0b990bbed79c1d16bfa8..3f6a094e0319092f3c8151408813cd2678468d85 100644 (file)
--- a/collect.h
+++ b/collect.h
@@ -34,8 +34,9 @@ private:
        vector<Display*> displays;
        int numSeqs, numGroupComb, totalNumSeq;
        string label, groupLabel;
        vector<Display*> displays;
        int numSeqs, numGroupComb, totalNumSeq;
        string label, groupLabel;

-       void getGroupComb();
+       void getGroupComb(vector<string>);

        vector<string> groupComb;
        vector<string> groupComb;

+       bool validGroup(vector<string>, string);

 };
 
 
 };
 
 

diff --git a/collectcommand.cpp b/collectcommand.cpp
index 0f622c49b2a30632f53e4fa3ec0dfc3196113374..f012ba151e0813f9b7ab67f5c2961db8eec23b1b 100644 (file)
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -36,6 +36,7 @@ CollectCommand::CollectCommand(){
                                }else if (globaldata->Estimators[i] == "chao") { 
                                        cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
                                }else if (globaldata->Estimators[i] == "ace") { 
                                }else if (globaldata->Estimators[i] == "chao") { 
                                        cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
                                }else if (globaldata->Estimators[i] == "ace") { 

+                               convert(globaldata->getAbund(), abund);

                                        cDisplays.push_back(new CollectDisplay(new Ace(), new ThreeColumnFile(fileNameRoot+"ace")));
                                }else if (globaldata->Estimators[i] == "jack") { 
                                        cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
                                        cDisplays.push_back(new CollectDisplay(new Ace(), new ThreeColumnFile(fileNameRoot+"ace")));
                                }else if (globaldata->Estimators[i] == "jack") { 
                                        cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));


@@ -88,11 +89,12 @@ int CollectCommand::execute(){
                
                order = globaldata->gorder;
                input = globaldata->ginput;
                
                order = globaldata->gorder;
                input = globaldata->ginput;

-                       
+               set<string> orderList;  
+               

                while(order != NULL){
                
                while(order != NULL){
                

+                       orderList.insert(order->getLabel());

                        if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
                        if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){

-                       

                                cCurve = new Collect(order, cDisplays);
                                convert(globaldata->getFreq(), freq);
                                cCurve->getCurve(freq);
                                cCurve = new Collect(order, cDisplays);
                                convert(globaldata->getFreq(), freq);
                                cCurve->getCurve(freq);


@@ -101,12 +103,14 @@ int CollectCommand::execute(){
                        
                                cout << order->getLabel() << '\t' << count << endl;
                        }
                        
                                cout << order->getLabel() << '\t' << count << endl;
                        }

-               

                        order = (input->getOrderVector());
                        count++;
                        order = (input->getOrderVector());
                        count++;

-               

                }
                }

-       
+               set<string>::iterator i;
+               for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i)
+                       if(orderList.count(*i) == 0)
+                               cout << "'" << *i << "'" << " is not a valid label.\n";
+               globaldata->clearLabels();

                for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }       
                return 0;
        }
                for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }       
                return 0;
        }

diff --git a/collectcommand.h b/collectcommand.h
index 686c4910c7f6e50fc572be4a4408d08d838b5933..64362ef61cdfdc18da9cb5b170a88ff9713d93c9 100644 (file)
--- a/collectcommand.h
+++ b/collectcommand.h
@@ -25,11 +25,11 @@
        The collect command generates a collector's curve from the given file.  
        The collect command can only be executed after a successful read.list, read.sabund or read.rabund command, with one exception. 
        The collect command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster.  
        The collect command generates a collector's curve from the given file.  
        The collect command can only be executed after a successful read.list, read.sabund or read.rabund command, with one exception. 
        The collect command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster.  

-       The collect command outputs a file for each estimator you choose to use.  The collect command parameters are label, line, freq, single.  
+       The collect command outputs a file for each estimator you choose to use.  The collect command parameters are label, line, freq, single, abund.  

        No parameters are required, but you may not use both the line and label  parameters at the same time.  
        No parameters are required, but you may not use both the line and label  parameters at the same time.  

-       The collect command should be in the following format: collect(label=yourLabel, line=yourLines, freq=yourFreq, single=yourEstimators). 
+       The collect command should be in the following format: collect(label=yourLabel, line=yourLines, freq=yourFreq, single=yourEstimators, abund=yourAbund). 

        example collect(label=unique-.01-.03, line=0,5,10, freq=10, single=collect-chao-ace-jack).  
        example collect(label=unique-.01-.03, line=0,5,10, freq=10, single=collect-chao-ace-jack).  

-       The default values for  freq is 100, and single are collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson.  
+       The default values for  freq is 100, for abund is 10, and single are collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson.  

        The valid single estimators are: collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson. 
        The label and line parameters are used to analyze specific lines in your input. */
 
        The valid single estimators are: collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson. 
        The label and line parameters are used to analyze specific lines in your input. */
 


@@ -52,7 +52,7 @@ private:
        Collect* cCurve;
        ValidCalculators* validCalculator;
        vector<Display*> cDisplays;
        Collect* cCurve;
        ValidCalculators* validCalculator;
        vector<Display*> cDisplays;

-       int freq;
+       int freq, abund;

 
 };
 
 
 };
 

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 217045a4a1fc5dc0c83986f3b3a0345b755e1f6c..b3f798145bc4de3abe460aa0e8dbccd8825178c6 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -108,9 +108,10 @@ int CollectSharedCommand::execute(){
                        SharedList = globaldata->gSharedList;
                        order = SharedList->getSharedOrderVector();
                }
                        SharedList = globaldata->gSharedList;
                        order = SharedList->getSharedOrderVector();
                }

-               
+               set<string> orderList;
+

                while(order != NULL){
                while(order != NULL){

-               
+                       orderList.insert(order->getLabel());

                        if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
                                //create collectors curve
                                cCurve = new Collect(order, cDisplays);
                        if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
                                //create collectors curve
                                cCurve = new Collect(order, cDisplays);


@@ -137,7 +138,11 @@ int CollectSharedCommand::execute(){
                        
                        count++;
                }
                        
                        count++;
                }

-       
+               set<string>::iterator i;
+               for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i)
+                       if(orderList.count(*i) == 0)
+                               cout << "'" << *i << "'" << " is not a valid label.\n";
+               globaldata->clearLabels();

                for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }       
                return 0;
        }
                for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }       
                return 0;
        }

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 0c1b3e075ee8ade15e0ea619463df962e9eac846..840eaaccc82c392de096729a5db32d7c72cdf08a 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -16,6 +16,9 @@
 #include "parselistcommand.h"
 #include "collectcommand.h"
 #include "collectsharedcommand.h"
 #include "parselistcommand.h"
 #include "collectcommand.h"
 #include "collectsharedcommand.h"

+#include "getgroupcommand.h"
+#include "getlabelcommand.h"
+#include "getlinecommand.h"

 #include "rarefactcommand.h"
 #include "summarycommand.h"
 #include "summarysharedcommand.h"
 #include "rarefactcommand.h"
 #include "summarycommand.h"
 #include "summarysharedcommand.h"


@@ -70,8 +73,11 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "summary.shared")                {       command = new SummarySharedCommand();           }
                else if(commandName == "unifrac.weighted")              {       command = new UnifracWeightedCommand();         }
                else if(commandName == "unifrac.unweighted")    {       command = new UnifracUnweightedCommand();       }
                else if(commandName == "summary.shared")                {       command = new SummarySharedCommand();           }
                else if(commandName == "unifrac.weighted")              {       command = new UnifracWeightedCommand();         }
                else if(commandName == "unifrac.unweighted")    {       command = new UnifracUnweightedCommand();       }

+               else if(commandName == "get.group")             {   command = new GetgroupCommand();        }
+               else if(commandName == "get.label")             {   command = new GetlabelCommand();        }
+               else if(commandName == "get.line")              {   command = new GetlineCommand();         }

                else                                                                                    {       command = new NoCommand();                                      }
                else                                                                                    {       command = new NoCommand();                                      }

-                       
+

                return command;
        }
        catch(exception& e) {
                return command;
        }
        catch(exception& e) {

diff --git a/errorchecking.cpp b/errorchecking.cpp
index 1d60a4a35a8e7252e8f318a4997f91abdf102a51..cc6cbf9d8d96ac90a55dc68d16d2ffa157079cb1 100644 (file)
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -8,6 +8,7 @@
  */
 
 #include "errorchecking.h"
  */
 
 #include "errorchecking.h"

+#include <math.h>

 
 /*******************************************************/
 
 
 /*******************************************************/
 


@@ -36,6 +37,127 @@ void ErrorCheck::refresh() {
        cutoff = globaldata->getCutOff();
        format = globaldata->getFormat();
        method = globaldata->getMethod();
        cutoff = globaldata->getCutOff();
        format = globaldata->getFormat();
        method = globaldata->getMethod();

+
+       
+       string p[] = {
+               "phylip",              //0
+               "column",             //1
+               "list",               //2
+               "rabund",             //3
+               "sabund",             //4
+               "name",               //5
+               "order",              //6
+               "group",              //7
+               "fasta",              //8
+               "treefile",           //9
+               "cutoff",             //10
+               "precision",          //11
+               "iters",              //12
+               "jumble",             //13
+               "freq",               //14
+               "method",             //15
+               "fileroot",           //16
+               "line",               //17
+               "label",              //18
+               "single",             //19
+               "rarefaction",        //20
+               "shared",             //21
+               "summary",            //22
+               "sharedrarefaction",  //23
+               "sharedsummary",      //24
+               "comparegroups",      //25
+               "abund",              //26
+               };
+       
+       string c0[] = {p[0],p[5],p[10],p[11]};
+       string c1[] = {p[2],p[6],p[7]}; 
+       string c2[] = {p[10],p[11],p[15]}; 
+       string c3[] = {p[8]};  
+       string c4[] = {p[14],p[17],p[18],p[19],p[26]};
+       string c5[] = {p[13],p[14],p[17],p[18],p[21],p[25]};
+       string c6[] = {""}; 
+       string c7[] = {""}; 
+       string c8[] = {""}; 
+       string c9[] = {p[12],p[14],p[17],p[18],p[20],p[26]};
+       string c10[] = {p[12],p[13],p[17],p[18],p[23]};
+       string c11[] = {p[17],p[18],p[22],p[26]};   
+       string c12[] =  {p[13],p[17],p[18],p[24]}; 
+       string c13[] = {""};    
+       
+       vector<string> v0 (c0, c0+sizeof(c0)/sizeof(string)); 
+       vector<string> v1 (c1, c1+sizeof(c1)/sizeof(string));
+       vector<string> v2 (c2, c2+sizeof(c2)/sizeof(string));
+       vector<string> v3 (c3, c3+sizeof(c3)/sizeof(string));
+       vector<string> v4 (c4, c4+sizeof(c4)/sizeof(string));
+       vector<string> v5 (c5, c5+sizeof(c5)/sizeof(string));
+       vector<string> v6 (c6, c6+sizeof(c6)/sizeof(string));
+       vector<string> v7 (c7, c7+sizeof(c7)/sizeof(string));
+       vector<string> v8 (c8, c8+sizeof(c8)/sizeof(string));
+       vector<string> v9 (c9, c9+sizeof(c9)/sizeof(string));
+       vector<string> v10 (c10, c10+sizeof(c10)/sizeof(string));
+       vector<string> v11 (c11, c11+sizeof(c11)/sizeof(string));
+       vector<string> v12 (c12, c12+sizeof(c12)/sizeof(string));
+       vector<string> v13 (c13, c13+sizeof(c13)/sizeof(string));
+       
+       vector<vector<string> > allCommands;
+       allCommands.push_back(v0);
+       allCommands.push_back(v1);
+       allCommands.push_back(v2);
+       allCommands.push_back(v3);
+       allCommands.push_back(v4);
+       allCommands.push_back(v5);
+       allCommands.push_back(v6);
+       allCommands.push_back(v7);
+       allCommands.push_back(v8);
+       allCommands.push_back(v9);
+       allCommands.push_back(v10);
+       allCommands.push_back(v11);
+       allCommands.push_back(v12);
+       allCommands.push_back(v13);
+       
+       string commands[] = {
+       "read.dist",          //0
+       "read.otu",           //1
+       "cluster",            //2
+       "deconvolute",        //3
+       "collect.single",     //4
+       "collect.shared",     //5
+       "get.group",          //6
+       "get.label",          //7
+       "get.line",           //8
+       "rarefaction.single", //9
+       "rarefaction.shared", //10
+       "summary.single",     //11
+       "summary.shared",     //12
+       "quit"                //13
+       };
+       
+       for(int i = 0; i < allCommands.size(); i++)
+               commandParameters[commands[i]] = allCommands.at(i);
+       
+        //{Lowerbound(piSent if no lowerbound), Upperbound(piSent if no upperbound), 1 if only the first 2 values, 0 if greater than, 0 if less than};
+       piSent = 3.14159;
+       double ip0[] = {10, piSent, 0, 1, 0};
+       double ip1[] = {10, piSent, 0, 1, 0};
+       double ip2[] = {0, 1, 1, 0, 0};
+       double ip3[] =  {1, piSent, 0, 0, 0};
+       double ip4[] = {1, piSent, 0, 1, 0};
+       double ip5[] = {5, piSent, 0, 1, 0};
+       
+       vector<double> ipv0 (ip0, ip0+sizeof(ip0)/sizeof(double)); 
+       vector<double> ipv1 (ip1, ip1+sizeof(ip1)/sizeof(double)); 
+       vector<double> ipv2 (ip2, ip2+sizeof(ip2)/sizeof(double)); 
+       vector<double> ipv3 (ip3, ip3+sizeof(ip3)/sizeof(double)); 
+       vector<double> ipv4 (ip4, ip4+sizeof(ip4)/sizeof(double)); 
+       vector<double> ipv5 (ip5, ip5+sizeof(ip5)/sizeof(double));
+
+       intParams[p[11]] = ipv0;
+       intParams[p[12]] = ipv1;
+       intParams[p[13]] = ipv2;
+       intParams[p[14]] = ipv3;
+       intParams[p[17]] = ipv4;
+       intParams[p[26]] = ipv5;
+       

        randomtree = globaldata->getRandomTree();
        sharedfile = globaldata->getSharedFile();
 }
        randomtree = globaldata->getRandomTree();
        sharedfile = globaldata->getSharedFile();
 }


@@ -73,6 +195,7 @@ bool ErrorCheck::checkInput(string input) {
                if (validCommand->isValidCommand(commandName) != true) { return false; }
                
                string parameter, value;
                if (validCommand->isValidCommand(commandName) != true) { return false; }
                
                string parameter, value;

+               

                //reads in parameters and values
                if((optionText != "") && (commandName != "help")){
                        while((optionText.find_first_of(',') != -1) && (errorFree)) {  //while there are parameters
                //reads in parameters and values
                if((optionText != "") && (commandName != "help")){
                        while((optionText.find_first_of(',') != -1) && (errorFree)) {  //while there are parameters


@@ -81,7 +204,48 @@ bool ErrorCheck::checkInput(string input) {
                                
                                //is it a valid parameter
                                if (validParameter->isValidParameter(parameter) != true) { return false; }
                                
                                //is it a valid parameter
                                if (validParameter->isValidParameter(parameter) != true) { return false; }

-                               
+                               if(!validCommandParameter(parameter,commandName)) { 
+                                       cout << "'" << parameter << "' is not a valid parameter for the " << commandName << " command.\n";
+                                       return false; 
+                               }
+                               if(!validParameterValue(value, parameter)) {
+                                       if(parameter.compare("precision") == 0)
+                                               cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n";
+                                       else {
+                                       vector<double> bounds = intParams[parameter];
+                                       double a = bounds.at(0);
+                                       double b = bounds.at(1);
+                                       double c = bounds.at(2);
+                                       double d = bounds.at(3);
+                                       double e = bounds.at(4);
+                                       cout << "The '" << parameter << "' parameter needs to be ";
+                                       if(c == 1)
+                                                       cout << "either '" << a << "' or '" << b << "'.\n";
+                                       else
+                                       {
+                                               if(a != piSent)
+                                               {
+                                                       cout << ">";
+                                                       if(d != 0)
+                                                               cout << "=";
+                                                       cout << " '" << a << "'";
+                                               }
+                                               if(b == piSent)
+                                                       cout << ".\n";
+                                               else if(a != piSent)
+                                                       cout << " and ";
+                                               if(b != piSent)
+                                               {
+                                                       cout << "<";
+                                                       if(e != 0)
+                                                               cout << "=";
+                                                       cout << " '" << b << ".\n";
+                                               }
+                                       }
+                                       }
+                                       return false;
+                               }
+

                                if (parameter == "phylip" )             { phylipfile = value; }
                                if (parameter == "column" )             { columnfile = value; }
                                if (parameter == "list" )               { listfile = value; }
                                if (parameter == "phylip" )             { phylipfile = value; }
                                if (parameter == "column" )             { columnfile = value; }
                                if (parameter == "list" )               { listfile = value; }


@@ -102,8 +266,14 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "fileroot" )           { fileroot = value; }
                                if (parameter == "line" )                       { line = value; }
                                if (parameter == "label" )                      { label = value; }
                                if (parameter == "fileroot" )           { fileroot = value; }
                                if (parameter == "line" )                       { line = value; }
                                if (parameter == "label" )                      { label = value; }

+                               if (parameter == "abund" )          { abund = value; }

                                if (parameter == "random" )                     { randomtree = value;   }
 
                                if (parameter == "random" )                     { randomtree = value;   }
 

+                               if (parameter == "comparegroups") { //stores groups to be compared
+                                       sharedGroups.clear(); //clears out old values
+                                       globaldata->splitAtDash(value, sharedGroups);
+                               }
+

                        }
                        
                        //gets the last parameter and value
                        }
                        
                        //gets the last parameter and value


@@ -112,7 +282,47 @@ bool ErrorCheck::checkInput(string input) {
                                splitAtEquals(parameter, value);
                                //is it a valid parameter
                                if (validParameter->isValidParameter(parameter) != true) { return false; }
                                splitAtEquals(parameter, value);
                                //is it a valid parameter
                                if (validParameter->isValidParameter(parameter) != true) { return false; }

-                               
+                               if(!validCommandParameter(parameter,commandName)) { 
+                                       cout << "'" << parameter << "' is not a valid parameter for the " << commandName << " command.\n";
+                                       return false; 
+                               }
+                               if(!validParameterValue(value, parameter)) {
+                                       if(parameter.compare("precision") == 0)
+                                               cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n";
+                                       else {
+                                       vector<double> bounds = intParams[parameter];
+                                       double a = bounds.at(0);
+                                       double b = bounds.at(1);
+                                       double c = bounds.at(2);
+                                       double d = bounds.at(3);
+                                       double e = bounds.at(4);
+                                       cout << "The '" << parameter << "' parameter needs to be ";
+                                       if(c == 1)
+                                                       cout << "either '" << a << "' or '" << b << "'.\n";
+                                       else
+                                       {
+                                               if(a != piSent)
+                                               {
+                                                       cout << ">";
+                                                       if(d != 0)
+                                                               cout << "=";
+                                                       cout << " '" << a << "'";
+                                               }
+                                               if(b == piSent)
+                                                       cout << ".\n";
+                                               else if(a != piSent)
+                                                       cout << " and ";
+                                               if(b != piSent)
+                                               {
+                                                       cout << "<";
+                                                       if(e != 0)
+                                                               cout << "=";
+                                                       cout << " '" << b << ".\n";
+                                               }
+                                       }
+                                       }
+                                       return false;
+                               }

                                if (parameter == "phylip" )             { phylipfile = value; }
                                if (parameter == "column" )             { columnfile = value; }                         
                                if (parameter == "list" )               { listfile = value; }
                                if (parameter == "phylip" )             { phylipfile = value; }
                                if (parameter == "column" )             { columnfile = value; }                         
                                if (parameter == "list" )               { listfile = value; }


@@ -134,7 +344,12 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "line" )                       { line = value; }
                                if (parameter == "label" )                      { label = value; }
                                if (parameter == "random" )                     { randomtree = value;   }
                                if (parameter == "line" )                       { line = value; }
                                if (parameter == "label" )                      { label = value; }
                                if (parameter == "random" )                     { randomtree = value;   }

+                               if (parameter == "abund" )          { abund = value; }

 
 

+                               if (parameter == "comparegroups") { //stores groups to be compared
+                                       sharedGroups.clear(); //clears out old values
+                                       globaldata->splitAtDash(value, sharedGroups);
+                               }

                        }
                }
                
                        }
                }
                


@@ -183,6 +398,12 @@ bool ErrorCheck::checkInput(string input) {
                }
                
                //check for valid method
                }
                
                //check for valid method

+               if(commandName == "get.group") {
+                       if ((globaldata->getGroupFile() == "")) { cout << "You must read a group before you can use the get.group command." << endl; return false; }
+               }
+               if (commandName == "get.label" || commandName == "get.line") {
+                       if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the get.label or get.line command." << endl; return false; }
+               }

                if (commandName == "cluster") {
                        if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
                        else {cout << "Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average." << endl; return false; }
                if (commandName == "cluster") {
                        if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
                        else {cout << "Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average." << endl; return false; }


@@ -198,7 +419,9 @@ bool ErrorCheck::checkInput(string input) {
                                else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; }
                        }
                }
                                else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; }
                        }
                }

- 
+
+               globaldata->clearAbund();
+

                return errorFree;
 }
 
                return errorFree;
 }
 


@@ -276,6 +499,113 @@ void ErrorCheck::validateReadFiles() {
 }
 /*******************************************************/
 
 }
 /*******************************************************/
 

+/******************************************************/
+//This function checks to see if the given paramter
+//is a valid paramter for the given command.
+bool ErrorCheck::validCommandParameter(string parameter, string commandName) {
+       try {
+               for(int i = 0; i < commandParameters[commandName].size(); i++)
+                       if(parameter.compare(commandParameters[commandName][i]) == 0)
+                               return true;
+               return false;
+       }
+               
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+}
+/*******************************************************/
+
+/******************************************************/
+//This function checks to see if the given paramter value
+//is convertable into an int if that parameter requires it.
+bool ErrorCheck::validParameterValue(string value, string parameter) {
+       try {
+               int pVal;
+               if(intParams.count(parameter) == 1)
+               {
+                       vector<double> bounds = intParams[parameter];
+                       bool valid = convertTest(value, pVal);
+                       if(!valid)
+                               return false;
+                       if(parameter.compare("precision") == 0)
+                       {
+                               double logNum = log10((double)pVal);
+                               double diff = (double)((int)logNum - logNum);
+                               if(diff != 0)
+                                       return false;
+                       }
+                       double a = bounds.at(0);
+                       double b = bounds.at(1);
+                       double c = bounds.at(2);
+                       double d = bounds.at(3);
+                       double e = bounds.at(4);
+                       bool a0 = pVal > a;
+                       bool a1 = pVal >= a;
+                       bool b0 = pVal < b;
+                       bool b1 = pVal <= b;
+                       
+                       if(c != 1)
+                       {
+                               if(a == piSent && b == piSent)
+                                       return true;
+                               if(a != piSent && b == piSent)
+                               {
+                                       if(d == 0)
+                                               return a0;
+                                       else
+                                               return a1;
+                               }
+                               else if(a == piSent && b != piSent)
+                               {
+                                       if(e == 0)
+                                               return b0;
+                                       else
+                                               return b1;
+                               }
+                               else
+                               {
+                                       if(d == 0 && e == 0)
+                                               return (a0 && b0);
+                                       else if(d == 0 && e == 1)
+                                               return (a0 && b1);
+                                       else if(d == 1 && e == 0)
+                                               return (a1 && b0);
+                                       else
+                                               return (a1 && b1);
+                               }
+                       }
+                       else
+                       {
+                               if(a == piSent && b == piSent)
+                                       return true;
+                               if(a != piSent && b == piSent)
+                                       return (pVal == a);
+                               else if(a == piSent && b != piSent)
+                                       return (pVal == b);
+                               else
+                                       return (pVal == a || pVal == b);
+                       }
+               }
+               return true;
+       }
+               
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+}              
+/*******************************************************/
+

 /******************************************************/
 //This function checks to make sure the user entered appropriate
 // format parameters on a distfile read
 /******************************************************/
 //This function checks to make sure the user entered appropriate
 // format parameters on a distfile read

diff --git a/errorchecking.h b/errorchecking.h
index 1b023e079cf8ab15c8539596dc72841be7edf7a3..8b3c0cafb0e6b787d5d408083828ab39757420bc 100644 (file)
--- a/errorchecking.h
+++ b/errorchecking.h
@@ -27,6 +27,8 @@ class ErrorCheck {
                ValidCommands* validCommand;
                ValidParameters* validParameter;
                void validateReadFiles();
                ValidCommands* validCommand;
                ValidParameters* validParameter;
                void validateReadFiles();

+               bool validCommandParameter(string, string);
+               bool validParameterValue(string, string);

                void validateReadDist();
                void validateReadPhil();
                void validateParseFiles();
                void validateReadDist();
                void validateReadPhil();
                void validateParseFiles();


@@ -34,9 +36,14 @@ class ErrorCheck {
                void clear();
                void refresh();
                string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, sharedfile, cutoff, format; 
                void clear();
                void refresh();
                string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, sharedfile, cutoff, format; 

-               string precision, method, fileroot, label, line, iters, jumble, freq, single, rarefaction, shared, summary, randomtree;
+               string precision, method, fileroot, label, line, iters, jumble, freq, single, rarefaction, shared, summary, randomtree, abund;

                string commandName, optionText;
                bool errorFree;
                string commandName, optionText;
                bool errorFree;

-               
+
+               vector<string> sharedGroups;
+               map <string, vector<string> > commandParameters;
+               map <string, vector<double> > intParams;
+               double piSent;
+

 };
 #endif
 };
 #endif

diff --git a/globaldata.cpp b/globaldata.cpp
index eeb1f4d5c51d36d5f38942f6c0b328a7386eb20b..66a44f25b7246af237194e634eeeeb9514623899 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -76,7 +76,6 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        gGroupmap = NULL;
                        gTree.clear();
                        labels.clear(); lines.clear(); groups.clear();
                        gGroupmap = NULL;
                        gTree.clear();
                        labels.clear(); lines.clear(); groups.clear();

-                       

                }
                
                //saves help request
                }
                
                //saves help request


@@ -109,9 +108,11 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                if (key == "freq" )                     { freq = value;                 }
                                if (key == "method" )           { method = value;               }
                                if (key == "fileroot" )         { fileroot = value;             }
                                if (key == "freq" )                     { freq = value;                 }
                                if (key == "method" )           { method = value;               }
                                if (key == "fileroot" )         { fileroot = value;             }

+                               if (key == "abund" )        { abund = value;        }

                                if (key == "random" )           { randomtree = value;   }
                                if (key == "groups" )           { groups = value;       }
                                if (key == "calc")                      { calc = value;         }
                                if (key == "random" )           { randomtree = value;   }
                                if (key == "groups" )           { groups = value;       }
                                if (key == "calc")                      { calc = value;         }

+

                                
                                if (key == "line") {//stores lines to be used in a set
                                        lines.clear();
                                
                                if (key == "line") {//stores lines to be used in a set
                                        lines.clear();


@@ -127,11 +128,13 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                        splitAtDash(value, labels);
                                        allLines = 0;
                                }
                                        splitAtDash(value, labels);
                                        allLines = 0;
                                }

+

                                if (key == "groups") {//stores groups to be used in a vector
                                        Groups.clear();
                                        groups = value;
                                        splitAtDash(value, Groups);
                                }
                                if (key == "groups") {//stores groups to be used in a vector
                                        Groups.clear();
                                        groups = value;
                                        splitAtDash(value, Groups);
                                }

+

                        }
                        
                        //saves the last parameter
                        }
                        
                        //saves the last parameter


@@ -155,6 +158,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        if (key == "freq" )                     { freq = value;                 }
                        if (key == "method" )           { method = value;               }
                        if (key == "fileroot" )         { fileroot = value;             }
                        if (key == "freq" )                     { freq = value;                 }
                        if (key == "method" )           { method = value;               }
                        if (key == "fileroot" )         { fileroot = value;             }

+                       if (key == "abund" )        { abund = value;        }

                        if (key == "random" )           { randomtree = value;   }
                        if (key == "groups" )           { groups = value;       }
                        if (key == "calc")                      { calc = value;         }
                        if (key == "random" )           { randomtree = value;   }
                        if (key == "groups" )           { groups = value;       }
                        if (key == "calc")                      { calc = value;         }


@@ -255,6 +259,7 @@ string GlobalData::getFileRoot()            {       return fileroot;        }
 string GlobalData::getIters()                  {       return iters;           }
 string GlobalData::getJumble()                 {       return jumble;          }
 string GlobalData::getFreq()                   {       return freq;            }
 string GlobalData::getIters()                  {       return iters;           }
 string GlobalData::getJumble()                 {       return jumble;          }
 string GlobalData::getFreq()                   {       return freq;            }

+string GlobalData::getAbund()           {   return abund;       }

 string GlobalData::getRandomTree()             {       return randomtree;      }
 void GlobalData::setListFile(string file)      {       listfile = file;        inputFileName = file;}
 void GlobalData::setRabundFile(string file)    {       rabundfile = file;      inputFileName = file;}
 string GlobalData::getRandomTree()             {       return randomtree;      }
 void GlobalData::setListFile(string file)      {       listfile = file;        inputFileName = file;}
 void GlobalData::setRabundFile(string file)    {       rabundfile = file;      inputFileName = file;}


@@ -302,9 +307,10 @@ void GlobalData::clear() {
        freq                    =       "100";
        method                  =       "furthest";
        fileroot                =       "";
        freq                    =       "100";
        method                  =       "furthest";
        fileroot                =       "";

-       calc                    =       "";
+       abund           =   "10";

 }
 }

-/*******************************************************/
+
+//*******************************************************/

 
 /******************************************************/
 void GlobalData::reset() {
 
 /******************************************************/
 void GlobalData::reset() {


@@ -319,6 +325,7 @@ void GlobalData::reset() {
        freq                    =       "100";
        method                  =       "furthest";
        calc                    =       "";
        freq                    =       "100";
        method                  =       "furthest";
        calc                    =       "";

+       abund = "10";

 }
 /*******************************************************/
 
 }
 /*******************************************************/
 


@@ -330,6 +337,3 @@ GlobalData::~GlobalData() {
        if(gorder != NULL)                      {       delete gorder;          }
 }
 /*******************************************************/
        if(gorder != NULL)                      {       delete gorder;          }
 }
 /*******************************************************/

-
-/******************************************************/
-

diff --git a/globaldata.hpp b/globaldata.hpp
index 277d351062fd67726f0ba05d53647d8c98b2a53c..b36545effa90467bbfeddab77c56351ebeea934a 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -41,10 +41,9 @@ public:
        TreeMap* gTreemap;
        string inputFileName, helpRequest, commandName;
        bool allLines;
        TreeMap* gTreemap;
        string inputFileName, helpRequest, commandName;
        bool allLines;

-       vector<string> Estimators; //holds estimators to be used
+       vector<string>  Estimators, Groups; //holds estimators to be used

        set<int> lines; //hold lines to be used
        set<string> labels; //holds labels to be used
        set<int> lines; //hold lines to be used
        set<string> labels; //holds labels to be used

-       vector<string> Groups;

        
        string getPhylipFile();
        string getColumnFile();
        
        string getPhylipFile();
        string getColumnFile();


@@ -65,7 +64,9 @@ public:
        string getIters();
        string getJumble();
        string getFreq();
        string getIters();
        string getJumble();
        string getFreq();

+       string getAbund();

        string getRandomTree();
        string getRandomTree();

+

        void setListFile(string);
        void setPhylipFile(string);
        void setColumnFile(string);
        void setListFile(string);
        void setPhylipFile(string);
        void setColumnFile(string);


@@ -79,11 +80,16 @@ public:
        
        void setListVector(ListVector*);
        void setSparseMatrix(SparseMatrix*);
        
        void setListVector(ListVector*);
        void setSparseMatrix(SparseMatrix*);

+       void clear(); 
+       void clearLabels();
+       void clearAbund();
+       

        void parseGlobalData(string, string);
                
 private:
        string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, sharedfile, line, label, randomtree, groups;
        void parseGlobalData(string, string);
                
 private:
        string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, sharedfile, line, label, randomtree, groups;

-       string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc;
+       string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund;
+

        static GlobalData* _uniqueInstance;
        GlobalData( const GlobalData& ); // Disable copy constructor
        void operator=( const GlobalData& ); // Disable assignment operator
        static GlobalData* _uniqueInstance;
        GlobalData( const GlobalData& ); // Disable copy constructor
        void operator=( const GlobalData& ); // Disable assignment operator

diff --git a/helpcommand.cpp b/helpcommand.cpp
index b627c140461d19713f39e3907d4d1a14a02b4414..206df13651075afac626139b30a917e1ae43562a 100644 (file)
--- a/helpcommand.cpp
+++ b/helpcommand.cpp
@@ -87,6 +87,25 @@ int HelpCommand::execute(){
                cout << "Example collect.shared(label=unique-.01-.03, line=0,5,10, freq=10, jumble=1, calc=sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN)." << "\n";
                cout << "The default values for jumble is 1 (meaning jumble, if it’s set to 0 then it will not jumble), freq is 100 and calc are sharedsobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN." << "\n";
                cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
                cout << "Example collect.shared(label=unique-.01-.03, line=0,5,10, freq=10, jumble=1, calc=sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN)." << "\n";
                cout << "The default values for jumble is 1 (meaning jumble, if it’s set to 0 then it will not jumble), freq is 100 and calc are sharedsobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN." << "\n";
                cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";

+               cout << "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile)." << "\n" << "\n";
+       }else if (globaldata->helpRequest == "get.group") {
+               cout << "The get.group command can only be executed after a successful read.otu command of a group file." << "\n";
+               cout << "You may not use any parameters with the get.group command." << "\n";
+               cout << "The get.group command should be in the following format: " << "\n";
+               cout << "get.group()" << "\n";
+               cout << "Example get.group()." << "\n";
+       }else if (globaldata->helpRequest == "get.label") {
+               cout << "The get.label command can only be executed after a successful read.otu command." << "\n";
+               cout << "You may not use any parameters with the get.label command." << "\n";
+               cout << "The get.label command should be in the following format: " << "\n";
+               cout << "get.label()" << "\n";
+               cout << "Example get.label()." << "\n";
+       }else if (globaldata->helpRequest == "get.line") {
+               cout << "The get.line command can only be executed after a successful read.otu command." << "\n";
+               cout << "You may not use any parameters with the get.line command." << "\n";
+               cout << "The get.line command should be in the following format: " << "\n";
+               cout << "get.line()" << "\n";
+               cout << "Example get.line()." << "\n";

                cout << "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq)." << "\n" << "\n";
        }else if (globaldata->helpRequest == "rarefaction.single") {
                cout << "The rarefaction.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION." << "\n";
                cout << "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq)." << "\n" << "\n";
        }else if (globaldata->helpRequest == "rarefaction.single") {
                cout << "The rarefaction.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION." << "\n";

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index 7e4ced55244665b4c3540f71491ce6dd4f003517..df33e5d7a01ed9ca053cee3849bd5bd1448bda23 100644 (file)
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -35,6 +35,9 @@ RareFactCommand::RareFactCommand(){
                                }else if (globaldata->Estimators[i] == "chao") { 
                                        rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao")));
                                }else if (globaldata->Estimators[i] == "ace") { 
                                }else if (globaldata->Estimators[i] == "chao") { 
                                        rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao")));
                                }else if (globaldata->Estimators[i] == "ace") { 

+                                       convert(globaldata->getAbund(), abund);
+                                       if(abund < 5)
+                                               abund = 10;

                                        rDisplays.push_back(new RareDisplay(new Ace(), new ThreeColumnFile(fileNameRoot+"r_ace")));
                                }else if (globaldata->Estimators[i] == "jack") { 
                                        rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));
                                        rDisplays.push_back(new RareDisplay(new Ace(), new ThreeColumnFile(fileNameRoot+"r_ace")));
                                }else if (globaldata->Estimators[i] == "jack") { 
                                        rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));

diff --git a/rarefactcommand.h b/rarefactcommand.h
index c81eb6fea19a3808ec93f0cdda1c779719947585..058d7dd2b6e0c0513b0d5c9697c29c68a2da61a3 100644 (file)
--- a/rarefactcommand.h
+++ b/rarefactcommand.h
@@ -52,7 +52,7 @@ private:
        InputData* input;
        ValidCalculators* validCalculator;
        Rarefact* rCurve;
        InputData* input;
        ValidCalculators* validCalculator;
        Rarefact* rCurve;

-       int freq, nIters;
+       int freq, nIters, abund;

 };
 
 #endif
 };
 
 #endif

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 7a3ad4a1e57e7f3f5dac9539fb2c974cd4e14cbe..06cc9b027de971c65204e3254ef07cc1eacae320 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -32,6 +32,9 @@ SummaryCommand::SummaryCommand(){
                                }else if(globaldata->Estimators[i] == "chao"){
                                        sumCalculators.push_back(new Chao1());
                                }else if(globaldata->Estimators[i] == "ace"){
                                }else if(globaldata->Estimators[i] == "chao"){
                                        sumCalculators.push_back(new Chao1());
                                }else if(globaldata->Estimators[i] == "ace"){

+                                       convert(globaldata->getAbund(), abund);
+                                       if(abund < 5)
+                                               abund = 10;

                                        sumCalculators.push_back(new Ace());
                                }else if(globaldata->Estimators[i] == "jack"){
                                        sumCalculators.push_back(new Jackknife());
                                        sumCalculators.push_back(new Ace());
                                }else if(globaldata->Estimators[i] == "jack"){
                                        sumCalculators.push_back(new Jackknife());

diff --git a/summarycommand.h b/summarycommand.h
index 8e2d74b0b52252250cd5cede8a1bf9b10a689449..4c5144c3d2213808ea416f3bf15d95566c6fa21b 100644 (file)
--- a/summarycommand.h
+++ b/summarycommand.h
@@ -49,5 +49,6 @@ private:
        SAbundVector* sabund;
        string outputFileName;
        ofstream outputFileHandle;
        SAbundVector* sabund;
        string outputFileName;
        ofstream outputFileHandle;

+       int abund;

 };
 #endif
 };
 #endif

diff --git a/utilities.hpp b/utilities.hpp
index bf7df2d6a96d5c294ef662ae2f1bd19bc11ff9b5..8f5009ffc4f0306a5da950e75a541aaa56cfb572 100644 (file)
--- a/utilities.hpp
+++ b/utilities.hpp
@@ -33,6 +33,19 @@ inline void convert(const string& s, T& x, bool failIfLeftoverChars = true){
        if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
                throw BadConversion(s);
 }
        if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
                throw BadConversion(s);
 }

+//**********************************************************************************************************************
+
+template<typename T>
+inline bool convertTest(const string& s, T& x, bool failIfLeftoverChars = true){
+       istringstream i(s);
+       char c;
+       if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
+       {
+               cout << "'" << s << "' is unable to be converted into an integer.\n";
+               return false;
+       } 
+       return true;
+}

 
 //**********************************************************************************************************************
 
 
 //**********************************************************************************************************************
 


@@ -285,8 +298,12 @@ inline void splitAtComma(string& prefix, string& suffix){
        try {
                prefix = suffix.substr(0,suffix.find_first_of(','));
                if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
        try {
                prefix = suffix.substr(0,suffix.find_first_of(','));
                if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string

-                       suffix = suffix.substr(suffix.find_first_of(',')+2, suffix.length());
+                       suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
+                       string space = " ";
+                       while(suffix.at(0) == ' ')
+                               suffix = suffix.substr(1, suffix.length());

                }
                }

+

        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the utilities class Function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the utilities class Function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";

diff --git a/validcommands.cpp b/validcommands.cpp
index 79b09d38dbad7325c8bbbff8e352a17d0ddaeaba..e0d604543ec564f1e364426a9f61c613e97ffea0 100644 (file)
--- a/validcommands.cpp
+++ b/validcommands.cpp
@@ -25,6 +25,9 @@ ValidCommands::ValidCommands() {
                commands["quit"]                                = "quit"; 
                commands["collect.single"]              = "collect.single"; 
                commands["collect.shared"]              = "collect.shared"; 
                commands["quit"]                                = "quit"; 
                commands["collect.single"]              = "collect.single"; 
                commands["collect.shared"]              = "collect.shared"; 

+               commands["get.group"]           = "get.group";
+               commands["get.label"]           = "get.label";
+               commands["get.line"]            = "get.line";

                commands["rarefaction.single"]  = "rarefaction.single"; 
                commands["rarefaction.shared"]  = "rarefaction.shared"; 
                commands["summary.single"]              = "summary.single"; 
                commands["rarefaction.single"]  = "rarefaction.single"; 
                commands["rarefaction.shared"]  = "rarefaction.shared"; 
                commands["summary.single"]              = "summary.single"; 

diff --git a/validparameter.cpp b/validparameter.cpp
index a82962f1e0096e406e7cc21d03dba08a3039ea3a..fca5c8e07fc50d9be08842e0787854431a6df4a9 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -30,7 +30,7 @@ ValidParameters::ValidParameters() {
                parameters["format"]                    = "format"; 
                parameters["precision"]                 = "precision"; 
                parameters["label"]                             = "label"; 
                parameters["format"]                    = "format"; 
                parameters["precision"]                 = "precision"; 
                parameters["label"]                             = "label"; 

-               parameters["line"]                              = "line"; 
+               parameters["line"]                              = "line";

                parameters["iters"]                             = "iters"; 
                parameters["jumble"]                    = "jumble"; 
                parameters["freq"]                              = "freq"; 
                parameters["iters"]                             = "iters"; 
                parameters["jumble"]                    = "jumble"; 
                parameters["freq"]                              = "freq"; 


@@ -40,10 +40,11 @@ ValidParameters::ValidParameters() {
                parameters["shared"]                    = "shared"; 
                parameters["summary"]                   = "summary"; 
                parameters["sharedsummary"]             = "sharedsummary";
                parameters["shared"]                    = "shared"; 
                parameters["summary"]                   = "summary"; 
                parameters["sharedsummary"]             = "sharedsummary";

+               parameters["abund"]             = "abund";

                parameters["random"]                    = "random";
                parameters["groups"]                    = "groups";
                parameters["calc"]                              = "calc";
                parameters["random"]                    = "random";
                parameters["groups"]                    = "groups";
                parameters["calc"]                              = "calc";

-               
+

        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function ValidParameters. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function ValidParameters. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";