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

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

diff --git a/binaries/src/clustalw/src/fileInput/GDEFileParser.cpp b/binaries/src/clustalw/src/fileInput/GDEFileParser.cpp
index 9df9a4a..e430d61 100644 (file)
--- a/binaries/src/clustalw/src/fileInput/GDEFileParser.cpp
+++ b/binaries/src/clustalw/src/fileInput/GDEFileParser.cpp
@@ -218,6 +218,12 @@ int GDEFileParser::countSeqs()
 void GDEFileParser::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];
@@ -289,7 +295,7 @@ void GDEFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>&
                 utilityObject->blankToUnderscore(_sname);
                 secStructName = string(_sname);
             
-                if (userParameters->getInteractive())
+                if (userParameters->getInteractive() && !userParameters->getGui())
                 {
                     strcpy(_title, "Found secondary structure in alignment file: ");
                     strcat(_title, _sname);
@@ -300,7 +306,7 @@ void GDEFileParser::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++)
@@ -371,7 +377,7 @@ void GDEFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>&
                 utilityObject->blankToUnderscore(_sname);
                 secStructName = string(_sname);
 
-                if (userParameters->getInteractive())
+                if (userParameters->getInteractive() && !userParameters->getGui())
                 {
                     strcpy(_title, "Found gap penalty mask in alignment file: ");
                     strcat(_title, _sname);
@@ -382,7 +388,7 @@ void GDEFileParser::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++)