*** empty log message ***

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index 4234d2dc65375ae5c2c56b75814494c15b566dab..2d070cb01bb545b31dc94224a0ab1fd3c1606f2f 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -37,16 +37,13 @@ bool ValidParameters::isValidParameter(string parameter, string command, string
                bool valid = false;
                vector<string> cParams = commandParameters[command];
                int numParams = cParams.size(); 
-               for(int i = 0; i < numParams; i++)
-               {
-                       if(cParams.at(i).compare(parameter) == 0)
-                       {
+               for(int i = 0; i < numParams; i++) {
+                       if(cParams.at(i).compare(parameter) == 0) {
                                valid = true;
                                i = numParams;
                        }
                }
-               if(!valid)
-               {
+               if(!valid) {
                        cout << "'" << parameter << "' is not a valid parameter for the " << command << " command.\n";
                        cout << "The valid paramters for the " << command << " command are: ";
                        for(int i = 0; i < numParams-1; i++)
@@ -65,8 +62,7 @@ bool ValidParameters::isValidParameter(string parameter, string command, string
                vector<string> values;
                splitAtDash(value, values);
                
-               for(int i = 0; i < values.size(); i++)
-               {
+               for(int i = 0; i < values.size(); i++) {
                        value = values.at(i);
                        valid = convertTest(value, pVal);
                
@@ -79,12 +75,10 @@ bool ValidParameters::isValidParameter(string parameter, string command, string
                                   Special Cases
                        *********************************************************************************************************/
                        
-                       if(parameter.compare("precision") == 0)
-                       {
+                       if(parameter.compare("precision") == 0) {
                                double logNum = log10((double)pVal);
                                double diff = (double)((int)logNum - logNum);
-                               if(diff != 0)
-                               {
+                               if(diff != 0) {
                                        cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n";
                                        return false;
                                }
@@ -110,8 +104,7 @@ bool ValidParameters::isValidParameter(string parameter, string command, string
                                c = 0;
                        else if(range.at(4).compare("only") == 0)
                                c = 1;
-                       else
-                       {
+                       else {
                                cout << "The range can only be 'between' or 'only' the bounding numbers.\n";
                                return false;
                        }
@@ -120,8 +113,7 @@ bool ValidParameters::isValidParameter(string parameter, string command, string
                                d = 0;
                        else if(range.at(0).compare(">=") == 0 || range[3].compare("=>") == 0)
                                d = 1;
-                       else
-                       {
+                       else {
                                cout << "The parameter value can only be '>', '>=', or '=>' the lower bounding number.\n";
                                return false;
                        }
@@ -130,8 +122,7 @@ bool ValidParameters::isValidParameter(string parameter, string command, string
                                e = 0;
                        else if(range.at(2).compare("<=") == 0 || range[4].compare("=<") == 0)
                                e = 1;
-                       else
-                       {
+                       else {
                                cout << "The parameter value can only be '<', '<=', or '=<' the upper bounding number.\n";
                                return false;
                        }
@@ -141,24 +132,20 @@ bool ValidParameters::isValidParameter(string parameter, string command, string
                        bool b0 = pVal < b;
                        bool b1 = pVal <= b;
                        
-                       if(c != 1)
-                       {
-                               if(a != piSentinel && b == piSentinel)
-                               {
+                       if(c != 1) {
+                               if(a != piSentinel && b == piSentinel) {
                                        if(d == 0)
                                                valid = a0;
                                        else
                                                valid = a1;
                                }
-                               else if(a == piSentinel && b != piSentinel)
-                               {
+                               else if(a == piSentinel && b != piSentinel) {
                                        if(e == 0)
                                                valid = b0;
                                        else
                                                valid = b1;
                                }
-                               else
-                               {
+                               else {
                                        if(d == 0 && e == 0)
                                                valid = (a0 && b0);
                                        else if(d == 0 && e == 1)
@@ -169,8 +156,7 @@ bool ValidParameters::isValidParameter(string parameter, string command, string
                                                valid = (a1 && b1);
                                }
                        }
-                       else
-                       {
+                       else {
                                if(a != piSentinel && b == piSentinel)
                                        valid = (pVal == a);
                                else if(a == piSentinel && b != piSentinel)
@@ -180,30 +166,26 @@ bool ValidParameters::isValidParameter(string parameter, string command, string
                        }
                        
                        
-                       if(!valid)
-                       {
+                       if(!valid) {
                                cout << "The '" << parameter << "' parameter needs to be ";
                                if(c == 1)
                                        cout << "either '" << a << "' or '" << b << "'.\n";
-                               else
-                               {
-                                       if(a != piSentinel)
-                                       {
+                               else {
+                                       if(a != piSentinel) {
                                                cout << ">";
                                                if(d != 0)
                                                        cout << "=";
                                                cout << " '" << a << "'";
                                        }
                                        if(b == piSentinel)
-                                               cout << ".\n";
+                                               cout << "'.\n";
                                        else if(a != piSentinel)
                                                cout << " and ";
-                                       if(b != piSentinel)
-                                       {
+                                       if(b != piSentinel) {
                                                cout << "<";
                                                if(e != 0)
                                                        cout << "=";
-                                               cout << " '" << b << ".\n";
+                                               cout << " '" << b << "'.\n";
                                        }
                                }
                                return false;
@@ -238,6 +220,9 @@ void ValidParameters::initCommandParameters() {
                string readtreeArray[] = {"tree","group"};
                commandParameters["read.tree"] = addParameters(readtreeArray, sizeof(readtreeArray)/sizeof(string));
                
+               string readseqsArray[] = {"fasta","phylip","clustal","nexus","line"};
+               commandParameters["read.seqs"] = addParameters(readseqsArray, sizeof(readseqsArray)/sizeof(string));
+               
                string clusterArray[] =  {"cutoff","precision","method"};
                commandParameters["cluster"] = addParameters(clusterArray, sizeof(clusterArray)/sizeof(string));
                
@@ -285,6 +270,9 @@ void ValidParameters::initCommandParameters() {
 
                string heatmapArray[] =  {"groups","line","label","sorted","scale"};
                commandParameters["heatmap"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
+               
+               string filterseqsArray[] =  {"trump", "soft", "filter"};
+               commandParameters["filter.seqs"] = addParameters(filterseqsArray, sizeof(filterseqsArray)/sizeof(string));
 
                string vennArray[] =  {"groups","line","label","calc"};
                commandParameters["venn"] = addParameters(vennArray, sizeof(vennArray)/sizeof(string));
@@ -345,7 +333,7 @@ void ValidParameters::initParameterRanges() {
                string jumbleArray[] = {">","0", "<","1", "only"};
                parameterRanges["jumble"] = addParameters(jumbleArray, rangeSize);
 
-               string freqArray[] = {">","1", "<","NA", "between"};
+               string freqArray[] = {">=","1", "<","NA", "between"};
                parameterRanges["freq"] = addParameters(freqArray, rangeSize);
 
                //string lineArray[] = {">=","1", "<","NA", "between"};
@@ -353,6 +341,9 @@ void ValidParameters::initParameterRanges() {
 
                string abundArray[] = {">=","5", "<","NA", "between"};
                parameterRanges["abund"] = addParameters(abundArray, rangeSize);
+               
+               string softArray[] = {">=","0", "<=","100", "between"};
+               parameterRanges["soft"] = addParameters(softArray, rangeSize);
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";