added help for alignment code and thomas' calcs to project

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 7bd433f6ba83e52aa7d9f842ca4b9adca4a5a304..d094ff2032723a14839e0cf6562985333f3ae82d 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -28,6 +28,9 @@
                373C691F0FC1C98600137ACD /* nast.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C691D0FC1C98600137ACD /* nast.cpp */; };
                373C692B0FC1C9EB00137ACD /* nastreport.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C69290FC1C9EB00137ACD /* nastreport.cpp */; };
                373C69340FC1CA9E00137ACD /* distancedb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C69320FC1CA9E00137ACD /* distancedb.cpp */; };
+               373C699A0FC1E63600137ACD /* boneh.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C69940FC1E63600137ACD /* boneh.cpp */; };
+               373C699B0FC1E63600137ACD /* efron.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C69960FC1E63600137ACD /* efron.cpp */; };
+               373C699C0FC1E63600137ACD /* solow.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C69980FC1E63600137ACD /* solow.cpp */; };
                374610780F40645300460C57 /* unifracweightedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374610770F40645300460C57 /* unifracweightedcommand.cpp */; };
                3746107E0F4064D100460C57 /* weighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3746107D0F4064D100460C57 /* weighted.cpp */; };
                374610830F40652400460C57 /* unweighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374610820F40652400460C57 /* unweighted.cpp */; };
@@ -211,6 +214,12 @@
                373C692A0FC1C9EB00137ACD /* nastreport.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nastreport.hpp; sourceTree = "<group>"; };
                373C69320FC1CA9E00137ACD /* distancedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distancedb.cpp; sourceTree = "<group>"; };
                373C69330FC1CA9E00137ACD /* distancedb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = distancedb.hpp; sourceTree = "<group>"; };
+               373C69940FC1E63600137ACD /* boneh.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = boneh.cpp; sourceTree = "<group>"; };
+               373C69950FC1E63600137ACD /* boneh.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = boneh.h; sourceTree = "<group>"; };
+               373C69960FC1E63600137ACD /* efron.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = efron.cpp; sourceTree = "<group>"; };
+               373C69970FC1E63600137ACD /* efron.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = efron.h; sourceTree = "<group>"; };
+               373C69980FC1E63600137ACD /* solow.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = solow.cpp; sourceTree = "<group>"; };
+               373C69990FC1E63600137ACD /* solow.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = solow.h; sourceTree = "<group>"; };
                374610760F40645300460C57 /* unifracweightedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unifracweightedcommand.h; sourceTree = "<group>"; };
                374610770F40645300460C57 /* unifracweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracweightedcommand.cpp; sourceTree = "<group>"; };
                3746107C0F4064D100460C57 /* weighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = weighted.h; sourceTree = "<group>"; };
@@ -621,6 +630,8 @@
                        isa = PBXGroup;
                        children = (
                                37D927BE0F21331F001D4494 /* calculator.h */,
+                               373C69950FC1E63600137ACD /* boneh.h */,
+                               373C69940FC1E63600137ACD /* boneh.cpp */,
                                3792948D0F2E271100B9034A /* treecalculator.h */,
                                37D927BD0F21331F001D4494 /* calculator.cpp */,
                                37D927B90F21331F001D4494 /* ace.h */,
@@ -638,6 +649,8 @@
                                37C753DF0FB3492400DBD02E /* dist.h */,
                                37C753F00FB34AE800DBD02E /* eachgapdist.h */,
                                37C753F40FB34C0300DBD02E /* eachgapignore.h */,
+                               373C69960FC1E63600137ACD /* efron.cpp */,
+                               373C69970FC1E63600137ACD /* efron.h */,
                                EB9303F70F53517300E8EF26 /* geom.h */,
                                EB9303F80F53517300E8EF26 /* geom.cpp */,
                                378C1AF10FB0644D004D63F5 /* goodscoverage.h */,
@@ -709,6 +722,8 @@
                                37D928410F21331F001D4494 /* simpson.h */,
                                37D928400F21331F001D4494 /* simpson.cpp */,
                                37D928430F21331F001D4494 /* sobs.h */,
+                               373C69980FC1E63600137ACD /* solow.cpp */,
+                               373C69990FC1E63600137ACD /* solow.h */,
                                374610810F40652400460C57 /* unweighted.h */,
                                374610820F40652400460C57 /* unweighted.cpp */,
                                37D9284E0F21331F001D4494 /* uvest.h */,
@@ -1069,6 +1084,9 @@
                                373C691F0FC1C98600137ACD /* nast.cpp in Sources */,
                                373C692B0FC1C9EB00137ACD /* nastreport.cpp in Sources */,
                                373C69340FC1CA9E00137ACD /* distancedb.cpp in Sources */,
+                               373C699A0FC1E63600137ACD /* boneh.cpp in Sources */,
+                               373C699B0FC1E63600137ACD /* efron.cpp in Sources */,
+                               373C699C0FC1E63600137ACD /* solow.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };

diff --git a/helpcommand.cpp b/helpcommand.cpp
index c259e1f065c5861c5fe337715bf5879e9709e1f9..9e433cdabb909e530f7f6dbe1324a3aff5298cb1 100644 (file)
--- a/helpcommand.cpp
+++ b/helpcommand.cpp
@@ -82,6 +82,22 @@ int HelpCommand::execute(){
                cout << "dist.seqs(fasta=yourFastaFile, calc=yourCalc, ends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) " << "\n";
                cout << "Example dist.seqs(fasta=amazon.fasta, calc=eachgap, ends=F, cutoff= 2.0, processors=3)." << "\n";
                cout << "Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc)." << "\n" << "\n";
+       }else if (globaldata->helpRequest == "align.seqs") {
+               cout << "The align.seqs command reads a file containing sequences and creates an alignment file and a report file." << "\n";
+               cout << "The align.seqs command parameters are fasta, phylip, clustal, nexus, template, search, ksize, align, match, mismatch, gapopen and gapextend.  " << "\n";
+               cout << "You must use one of the following parameters for your candidate filename: fasta, phylip, clustal or nexus. " << "\n";
+               cout << "The template parameter is also required." << "\n";
+               cout << "The search parameter allows you to specify the method to find most similar template.  Your options are: suffix, kmer, blast and distance. The default is suffix." << "\n";
+               cout << "The align parameter allows you to specify the alignment method to use.  Your options are: gotoh, needleman, blast and noalign. The default is blast." << "\n";
+               cout << "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 7." << "\n";
+               cout << "The match parameter allows you to specify the bonus for having the same base. The default is 1.0." << "\n";
+               cout << "The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0." << "\n";
+               cout << "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -5.0." << "\n";
+               cout << "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -2.0." << "\n";
+               cout << "The align.seqs command should be in the following format: " << "\n";
+               cout << "align.seqs(fasta=yourFastaFile, template=yourTemplateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) " << "\n";
+               cout << "Example align.seqs(fasta=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)" << "\n";
+               cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n";
        }else if (globaldata->helpRequest == "collect.single") {
                cout << "The collect.single command can only be executed after a successful read.otu command. WITH ONE EXECEPTION. " << "\n";
                cout << "The collect.single command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster." << "\n";

diff --git a/validparameter.cpp b/validparameter.cpp
index 1a1555df410d25f18b11176ffe2fb5aa0f1af6d6..3e4d16bb77fe04911bc9c50553a431aae99b4849 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -291,7 +291,7 @@ void ValidParameters::initCommandParameters() {
                string distanceArray[] =  {"fasta","phylip","clustal","nexus", "calc", "ends", "cutoff", "processors"};
                commandParameters["dist.seqs"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string));
                
-               string AlignArray[] =  {"fasta","phylip","clustal","nexus", "template", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"};
+               string AlignArray[] =  {"fasta","phylip","clustal","nexus", "template", "search", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"};
                commandParameters["align.seqs"] = addParameters(AlignArray, sizeof(AlignArray)/sizeof(string));
                
                string quitArray[] = {};