JWS-112 Bumping version of ClustalW (src, binaries and windows) to version 2.1.

[jabaws.git] / binaries / src / clustalw / src / fileInput / RSFFileParser.cpp

diff --git a/binaries/src/clustalw/src/fileInput/RSFFileParser.cpp b/binaries/src/clustalw/src/fileInput/RSFFileParser.cpp
index 9662f50..b76f8af 100644 (file)
--- a/binaries/src/clustalw/src/fileInput/RSFFileParser.cpp
+++ b/binaries/src/clustalw/src/fileInput/RSFFileParser.cpp
@@ -240,6 +240,12 @@ int RSFFileParser::countSeqs()
 void RSFFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>& secStructMask,
                      string& secStructName, int &structPenalties, int length)
 {
+    bool guigetss = false;
+    if(userParameters->getProfileNum() == 1 && userParameters->getStructPenalties1())
+         guigetss = true;
+    if(userParameters->getProfileNum() == 2 && userParameters->getStructPenalties2())
+         guigetss = true;
+
     char _title[MAXLINE + 1];
     char _line[MAXLINE + 1];
     char _lin2[MAXLINE + 1];
@@ -307,7 +313,7 @@ void RSFFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>&
             {
                 if (keyword(_line, "feature"))
                 {
-                    if (userParameters->getInteractive())
+                    if (userParameters->getInteractive() && !userParameters->getGui())
                     {
                         strcpy(_title, "Found secondary structure in alignment file: ");
                         strcat(_title, _sname);
@@ -318,7 +324,7 @@ void RSFFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>&
                     {
                         (*_lin2) = 'y';
                     }
-                    if ((*_lin2 != 'n') && (*_lin2 != 'N'))
+                    if (guigetss || ((*_lin2 != 'n') && (*_lin2 != 'N')))
                     {
                         structPenalties = SECST;
                         secStructMask.assign(length, '.');