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

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

diff --git a/binaries/src/clustalw/src/fileInput/EMBLFileParser.cpp b/binaries/src/clustalw/src/fileInput/EMBLFileParser.cpp
index 357524f..f33cc92 100644 (file)
--- a/binaries/src/clustalw/src/fileInput/EMBLFileParser.cpp
+++ b/binaries/src/clustalw/src/fileInput/EMBLFileParser.cpp
@@ -240,6 +240,12 @@ int EMBLFileParser::countSeqs()
  */
 void EMBLFileParser::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];
@@ -298,7 +304,7 @@ void EMBLFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>&
                     sscanf(_line + 2, "%s", _feature);
                     if (strcmp(_feature, "HELIX") == 0 || strcmp(_feature, "STRAND") == 0)
                     {
-                        if (userParameters->getInteractive())
+                        if (userParameters->getInteractive() && !userParameters->getGui())
                         {
                             strcpy(_title,
                                 "Found secondary structure in alignment file: ");
@@ -310,7 +316,7 @@ void EMBLFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>&
                         {
                             (*_lin2) = 'y';
                         }
-                        if ((*_lin2 != 'n') && (*_lin2 != 'N'))
+                        if (guigetss || ((*_lin2 != 'n') && (*_lin2 != 'N')))
                         {
                             structPenalties = SECST;
                             for (i = 0; i < length; i++)
@@ -348,7 +354,7 @@ void EMBLFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>&
                     {
                         (*_lin2) = 'y';
                     }
-                    if ((*_lin2 != 'n') && (*_lin2 != 'N'))
+                    if (guigetss || ((*_lin2 != 'n') && (*_lin2 != 'N')))
                     {
                         structPenalties = GMASK;
                         for (i = 0; i < length; i++)