[Phylobase-commits] r752 - pkg/src

[noreply at r-forge.r-project.org]

Author: francois
Date: 2010-03-11 23:34:21 +0100 (Thu, 11 Mar 2010)
New Revision: 752

Modified:
   pkg/src/NCLInterface.cpp
Log:
(1) allow option return.labels, (2) changes in the way the string is formatted to allow levels.uniform to work properly, (3) fixes bug with option polymorphic.convert, (4) changes in the way the string is formatted for polymorphic.convert

Modified: pkg/src/NCLInterface.cpp
===================================================================
--- pkg/src/NCLInterface.cpp	2010-03-11 22:30:57 UTC (rev 751)
+++ pkg/src/NCLInterface.cpp	2010-03-11 22:34:21 UTC (rev 752)
@@ -46,7 +46,8 @@
   NxsCharactersBlock &characters,
   bool allchar,
   bool polymorphictomissing,
-  bool levelsall) const
+  bool levelsall,
+  bool returnlabels) const
 {
 
 	int nchartoreturn = 0;
@@ -97,37 +98,29 @@
 							nexuscharacters+="NA";
 						}
 						else {
+							nexuscharacters+='"';
 							nexuscharacters+='{';
 							for (unsigned int k=0;k<characters.GetNumStates(taxon,character);k++) {
-								nexuscharacters+=characters.GetInternalRepresentation(taxon,character,0);
+								nexuscharacters+=characters.GetInternalRepresentation(taxon,character,k);	
 								if (k+1<characters.GetNumStates(taxon,character)) {
 									nexuscharacters+=',';
 								}
 							}
 							nexuscharacters+='}';
+							nexuscharacters+='"';
 						}
 					}
 					else {
+						nexuscharacters+='"';
 						nexuscharacters+=statenumber;
+						nexuscharacters+='"';
 					}
 					if (taxon+1<ntax) {
 						nexuscharacters+=',';
 					}
 				}
 				nexuscharacters+=')';
-				if (levelsall) {
-					nexuscharacters+=", levels=c(";
-					for (unsigned int l=0;l<characters.GetMaxObsNumStates(); l++) {
-						nexuscharacters+=l;
-						if (l+1<characters.GetMaxObsNumStates()) {
-							nexuscharacters+=',';
-						}
-					}
-					nexuscharacters+=')';
-				}
-				else {
-
-					NxsString levels=", levels=c(";
+				if (returnlabels) {
 					NxsString labels=", labels=c(";
 					unsigned int totallabellength=0;
 					for (unsigned int l=0;l<characters.GetObsNumStates(character); l++) {
@@ -135,20 +128,49 @@
 						labels+= characters.GetStateLabel(character,l);
 						totallabellength+=(characters.GetStateLabel(character,l)).length();
 						labels+='"';
-						levels+= l;
 						if (l+1<characters.GetObsNumStates(character)) {
-							labels+=',';
-							levels+=',';
+								labels+=',';
 						}
 					}
-					levels+=')';
 					labels+=')';
-					//cout<<"labels.length="<<labels.length()<<endl<<"levels.length="<<levels.length()<<endl<<"total label length="<<totallabellength<<endl;
 					if (totallabellength>characters.GetObsNumStates(character)) {
-						nexuscharacters+=levels;
 						nexuscharacters+=labels;
 					}
 				}
+				//if (levelsall) {
+				//	nexuscharacters+=", levels=c(";
+				//	for (unsigned int l=0;l<characters.GetMaxObsNumStates(); l++) {
+				//		nexuscharacters+=l;
+				//		if (l+1<characters.GetMaxObsNumStates()) {
+				//			nexuscharacters+=',';
+				//		}
+				//	}
+				//	nexuscharacters+=')';
+				//}
+				//else {
+				//
+				//	NxsString levels=", levels=c(";
+				//	NxsString labels=", labels=c(";
+				//	unsigned int totallabellength=0;
+				//	for (unsigned int l=0;l<characters.GetObsNumStates(character); l++) {
+				//		labels+='"';
+				//		labels+= characters.GetStateLabel(character,l);
+				//		totallabellength+=(characters.GetStateLabel(character,l)).length();
+				//		labels+='"';
+				//		levels+= l;
+				//		if (l+1<characters.GetObsNumStates(character)) {
+				//			labels+=',';
+				//			levels+=',';
+				//		}
+				//	}
+				//	levels+=')';
+				//	labels+=')';
+					//cout<<"labels.length="<<labels.length()<<endl<<"levels.length="<<levels.length()<<endl<<"total label length="<<totallabellength<<endl;
+				//	if (totallabellength>characters.GetObsNumStates(character)) {
+				//		nexuscharacters+=levels;
+				//		nexuscharacters+=labels;
+				//	}
+				//}
 				nexuscharacters+=")\n";
 			}
 			nexuscharacters+=", row.names=c(";
@@ -452,7 +474,7 @@
 }
 
 
-void BASICCMDLINE::RReturnCharacters(NxsString & outputstring, bool allchar, bool polymorphictomissing, bool levelsall)
+void BASICCMDLINE::RReturnCharacters(NxsString & outputstring, bool allchar, bool polymorphictomissing, bool levelsall, bool returnlabels)
 {
 	if (!nexusReader)
 		return;
@@ -465,7 +487,7 @@
 		for (unsigned i = 0; i < nCharBlocks; ++i) {
 			NxsCharactersBlock * cb = nexusReader->GetCharactersBlock(tb, i);
 			if (cb) {
-				AppendRContent(outputstring, *cb, allchar, polymorphictomissing, levelsall);
+				AppendRContent(outputstring, *cb, allchar, polymorphictomissing, levelsall, returnlabels);
 			}
 		}
 	}
@@ -2211,7 +2233,7 @@
 		basiccmdline.Initialize(argv[i]);
 	}
 	NxsString t;
-	basiccmdline.RReturnCharacters(t, true, false, false);
+	basiccmdline.RReturnCharacters(t, true, false, false, false);
 	if (!t.empty())
 		cout << t << '\n';
 	t.clear();