documentation

diff --git a/coverage.cpp b/coverage.cpp
index cd8138d7dd6216e31f0617a45cb7b0bd63d5dbb5..6b514fbc2e47a40c8312ecfa206bc4d9e04a1e50 100644 (file)
--- a/coverage.cpp
+++ b/coverage.cpp
@@ -7,6 +7,12 @@
  *
  */
 
+/* This class library coverage at the given distances of the Cramer-von Mises statistic.
+       you may refer to the "Integration of Microbial Ecology and Statistics: A Test To Compare Gene Libraries" 
+       paper in Applied and Environmental Microbiology, Sept. 2004, p. 5485-5492 0099-2240/04/$8.00+0  
+       DOI: 10.1128/AEM.70.9.5485-5492.2004 Copyright 2004 American Society for Microbiology for more information. */
+       
+       
 #include "coverage.h"
 
 //**********************************************************************************************************************

diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp
index 9ab9108f23ca4d63c3479bb8c6a27d27e08704ea..a51b3270f855062a0e2ee92fab63779b38b50877 100644 (file)
--- a/libshuffcommand.cpp
+++ b/libshuffcommand.cpp
@@ -7,6 +7,12 @@
  *
  */
 
+/* This class is designed to implement an integral form of the Cramer-von Mises statistic.
+       you may refer to the "Integration of Microbial Ecology and Statistics: A Test To Compare Gene Libraries" 
+       paper in Applied and Environmental Microbiology, Sept. 2004, p. 5485-5492 0099-2240/04/$8.00+0  
+       DOI: 10.1128/AEM.70.9.5485-5492.2004 Copyright 2004 American Society for Microbiology for more information. */
+
+
 #include "libshuffcommand.h"
 
 //**********************************************************************************************************************
@@ -108,7 +114,7 @@ int LibShuffCommand::execute(){
                                        //don't save AA to AA
                                        if (i != j) {
                                                //(Caa - Cab)^2
-                                               deltaValues[p].push_back( (abs(cValues[p][i][i]-cValues[p][i][j]) * abs(cValues[p][i][i]-cValues[p][i][j])) ); 
+                                               deltaValues[p].push_back((cValues[p][i][i]-cValues[p][i][j]) * (cValues[p][i][i]-cValues[p][i][j]));
                                                sumDelta[count] += deltaValues[p][count];
                                                count++;
                                        }
@@ -146,24 +152,18 @@ int LibShuffCommand::execute(){
                                                //don't save AA to AA
                                                if (i != j) {
                                                        //(Caa - Cab)^2
-                                                       rsumDelta[count][m] += ((abs(cValues[p][i][i]-cValues[p][i][j]) * abs(cValues[p][i][i]-cValues[p][i][j])));
+                                                       rsumDelta[count][m] += ((cValues[p][i][i]-cValues[p][i][j]) * (cValues[p][i][i]-cValues[p][i][j]));
                                                        count++;
                                                }
                                        }
                                }
                                
                        }
-//cout << "iter " << m << endl;
+
                        //clear out old Values
                        reading->update(m);
                        cValues.clear();
                        
-//cout << "random sum delta for iter " << m << endl;
-//for (int i = 0; i < rsumDelta.size(); i++) {
-//     cout << setprecision(6) << rsumDelta[i][m] << '\t';
-//}
-//cout << endl;
-
                }
                
                reading->finish();

diff --git a/validparameter.cpp b/validparameter.cpp
index efbd0a445d996c2f4f8b424a6f703057dab252e3..61fd0445e81f9ae277f3c54f9c69ce313646e66d 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -52,7 +52,7 @@ bool ValidParameters::isValidParameter(string parameter, string command) {
                        if ((readdist.find(parameter)) != (readdist.end())) {
                                return true;
                        }else { 
-                               cout << parameter << " is not a valid parameter for the read.dist command. Valid parameters are ";
+                               cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
                                for (it = readdist.begin(); it != readdist.end(); it++) {
                                        cout << it->first << ", ";
                                }
@@ -63,7 +63,7 @@ bool ValidParameters::isValidParameter(string parameter, string command) {
                        if ((readotu.find(parameter)) != (readotu.end())) {
                                return true;
                        }else { 
-                               cout << parameter << " is not a valid parameter for the read.otu command. Valid parameters are ";
+                               cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
                                for (it = readotu.begin(); it != readotu.end(); it++) {
                                        cout << it->first << ", ";
                                }
@@ -75,7 +75,7 @@ bool ValidParameters::isValidParameter(string parameter, string command) {
                        if ((readtree.find(parameter)) != (readtree.end())) {
                                return true;
                        }else { 
-                               cout << parameter << " is not a valid parameter for the read.tree command. Valid parameters are ";
+                               cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
                                for (it = readtree.begin(); it != readtree.end(); it++) {
                                        cout << it->first << ", ";
                                }
@@ -87,7 +87,7 @@ bool ValidParameters::isValidParameter(string parameter, string command) {
                        if ((cluster.find(parameter)) != (cluster.end())) {
                                return true;
                        }else { 
-                               cout << parameter << " is not a valid parameter for the cluster command. Valid parameters are ";
+                               cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
                                for (it = cluster.begin(); it != cluster.end(); it++) {
                                        cout << it->first << ", ";
                                }
@@ -98,7 +98,7 @@ bool ValidParameters::isValidParameter(string parameter, string command) {
                        if ((deconvolute.find(parameter)) != (deconvolute.end())) {
                                return true;
                        }else { 
-                               cout << parameter << " is not a valid parameter for the deconvolute command. Valid parameter is ";
+                               cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
                                for (it = deconvolute.begin(); it != deconvolute.end(); it++) {
                                        cout << it->first;
                                }
@@ -109,7 +109,7 @@ bool ValidParameters::isValidParameter(string parameter, string command) {
                        if ((parsimony.find(parameter)) != (parsimony.end())) {
                                return true;
                        }else { 
-                               cout << parameter << " is not a valid parameter for the parsimony command. Valid parameters are ";
+                               cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
                                for (it = parsimony.begin(); it != parsimony.end(); it++) {
                                        cout << it->first << ", ";
                                }
@@ -120,7 +120,7 @@ bool ValidParameters::isValidParameter(string parameter, string command) {
                        if ((collectsingle.find(parameter)) != (collectsingle.end())) {
                                return true;
                        }else { 
-                               cout << parameter << " is not a valid parameter for the collect.single command. Valid parameters are ";
+                               cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
                                for (it = collectsingle.begin(); it != collectsingle.end(); it++) {
                                        cout << it->first << ", ";
                                }
@@ -131,7 +131,7 @@ bool ValidParameters::isValidParameter(string parameter, string command) {
                        if ((collectshared.find(parameter)) != (collectshared.end())) {
                                return true;
                        }else { 
-                               cout << parameter << " is not a valid parameter for the collect.shared command. Valid parameters are ";
+                               cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
                                for (it = collectshared.begin(); it != collectshared.end(); it++) {
                                        cout << it->first << ", ";
                                }
@@ -142,7 +142,7 @@ bool ValidParameters::isValidParameter(string parameter, string command) {
                        if ((rarefactsingle.find(parameter)) != (rarefactsingle.end())) {
                                return true;
                        }else { 
-                               cout << parameter << " is not a valid parameter for the rarefaction.single command. Valid parameters are ";
+                               cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
                                for (it = rarefactsingle.begin(); it != rarefactsingle.end(); it++) {
                                        cout << it->first << ", ";
                                }
@@ -153,7 +153,7 @@ bool ValidParameters::isValidParameter(string parameter, string command) {
                        if ((rarefactshared.find(parameter)) != (rarefactshared.end())) {
                                return true;
                        }else { 
-                               cout << parameter << " is not a valid parameter for the rarefaction.shared command. Valid parameters are ";
+                               cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
                                for (it = rarefactshared.begin(); it != rarefactshared.end(); it++) {
                                        cout << it->first << ", ";
                                }
@@ -164,7 +164,7 @@ bool ValidParameters::isValidParameter(string parameter, string command) {
                        if ((summarysingle.find(parameter)) != (summarysingle.end())) {
                                return true;
                        }else { 
-                               cout << parameter << " is not a valid parameter for the summary.single command. Valid parameters are ";
+                               cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
                                for (it = summarysingle.begin(); it != summarysingle.end(); it++) {
                                        cout << it->first << ", ";
                                }
@@ -175,7 +175,7 @@ bool ValidParameters::isValidParameter(string parameter, string command) {
                        if ((summaryshared.find(parameter)) != (summaryshared.end())) {
                                return true;
                        }else { 
-                               cout << parameter << " is not a valid parameter for the summary.shared command. Valid parameters are ";
+                               cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
                                for (it = summaryshared.begin(); it != summaryshared.end(); it++) {
                                        cout << it->first << ", ";
                                }
@@ -186,7 +186,7 @@ bool ValidParameters::isValidParameter(string parameter, string command) {
                        if ((unifracweighted.find(parameter)) != (unifracweighted.end())) {
                                return true;
                        }else { 
-                               cout << parameter << " is not a valid parameter for the unifrac.weighted command. Valid parameters are ";
+                               cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
                                for (it = unifracweighted.begin(); it != unifracweighted.end(); it++) {
                                        cout << it->first << ", ";
                                }
@@ -197,7 +197,7 @@ bool ValidParameters::isValidParameter(string parameter, string command) {
                        if ((unifracunweighted.find(parameter)) != (unifracunweighted.end())) {
                                return true;
                        }else { 
-                               cout << parameter << " is not a valid parameter for the unifrac.unweighted command. Valid parameters are ";
+                               cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
                                for (it = unifracunweighted.begin(); it != unifracunweighted.end(); it++) {
                                        cout << it->first << ", ";
                                }
@@ -208,18 +208,18 @@ bool ValidParameters::isValidParameter(string parameter, string command) {
                        if ((libshuff.find(parameter)) != (libshuff.end())) {
                                return true;
                        }else { 
-                               cout << parameter << " is not a valid parameter for the libshuff command. Valid parameters are ";
+                               cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
                                for (it = libshuff.begin(); it != libshuff.end(); it++) {
                                        cout << it->first << ", ";
                                }
                                cout << endl;
                                return false; }
                //not a valid paramter
-               }else if (command == "help") { cout << parameter << " is not a valid parameter for the help command. There are no vaild parameters.";  
-               }else if (command == "quit") { cout << parameter << " is not a valid parameter for the quit command. There are no vaild parameters."; 
-               }else if (command == "get.group") { cout << parameter << " is not a valid parameter for the get.group command. There are no vaild parameters."; 
-               }else if (command == "get.label") { cout << parameter << " is not a valid parameter for the get.label command. There are no vaild parameters."; 
-               }else if (command == "get.line") { cout << parameter << " is not a valid parameter for the get.line command. There are no vaild parameters.";  }
+               }else if (command == "help") { cout << parameter << " is not a valid parameter for the " + command + " command. There are no vaild parameters." << endl;  
+               }else if (command == "quit") { cout << parameter << " is not a valid parameter for the " + command + " command. There are no vaild parameters." << endl; 
+               }else if (command == "get.group") { cout << parameter << " is not a valid parameter for the " + command + " command. There are no vaild parameters." << endl; 
+               }else if (command == "get.label") { cout << parameter << " is not a valid parameter for the " + command + " command. There are no vaild parameters." << endl; 
+               }else if (command == "get.line") { cout << parameter << " is not a valid parameter for the " + command + " command. There are no vaild parameters." << endl; }
                
                return false;