added mothurOutJustToScreen function and changed all counter outputs to use it.

[mothur.git] / filterseqscommand.h

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 4405c33f52165d5c89cbe47e8513147cb14dd879..ed7cfd1f98ddb6f44c8c7f690447d8dea1d4f6f0 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -24,7 +24,9 @@ public:
        vector<string> setParameters();\r
        string getCommandName()                 { return "filter.seqs";                 }\r
        string getCommandCategory()             { return "Sequence Processing"; }\r
+       \r
        string getHelpString(); \r
+    string getOutputPattern(string);   \r
        string getCitation() { return "http://www.mothur.org/wiki/Filter.seqs"; }\r
        string getDescription()         { return "removes columns from alignments based on a criteria defined by the user"; }\r
        \r
@@ -151,7 +153,7 @@ static DWORD WINAPI MyCreateFilterThreadFunction(LPVOID lpParam){
                        in.seekg(pDataArray->start-1); pDataArray->m->gobble(in); \r
                }\r
                \r
-               pDataArray->count = pDataArray->end;\r
+               pDataArray->count = 0;\r
                for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process\r
                        \r
                        if (pDataArray->m->control_pressed) { in.close(); pDataArray->count = 1; return 1; }\r
@@ -164,12 +166,12 @@ static DWORD WINAPI MyCreateFilterThreadFunction(LPVOID lpParam){
                 if(pDataArray->trump != '*')                   {       pDataArray->F.doTrump(current);         }\r
                 if(pDataArray->m->isTrue(pDataArray->vertical) || pDataArray->soft != 0)       {       pDataArray->F.getFreqs(current);        }\r
                        }\r
-            \r
+            pDataArray->count++;\r
             //report progress\r
-                       if((i) % 100 == 0){     pDataArray->m->mothurOut(toString(i)); pDataArray->m->mothurOutEndLine();               }\r
+                       if((i) % 100 == 0){     pDataArray->m->mothurOutJustToScreen(toString(i)+"\n");                 }\r
                }\r
                \r
-        if((pDataArray->count) % 100 != 0){    pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();               }\r
+        if((pDataArray->count) % 100 != 0){    pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count)+"\n");                 }\r
         \r
                in.close();\r
                \r
@@ -201,7 +203,7 @@ static DWORD WINAPI MyRunFilterThreadFunction(LPVOID lpParam){
                        in.seekg(pDataArray->start-1); pDataArray->m->gobble(in); \r
                }\r
                \r
-               pDataArray->count = pDataArray->end;\r
+               pDataArray->count = 0;\r
                for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process\r
                        \r
                        if (pDataArray->m->control_pressed) { in.close(); out.close(); pDataArray->count = 1; return 1; }\r
@@ -219,12 +221,12 @@ static DWORD WINAPI MyRunFilterThreadFunction(LPVOID lpParam){
                 \r
                 out << '>' << seq.getName() << endl << filterSeq << endl;\r
             }\r
-            \r
+            pDataArray->count++;\r
             //report progress\r
-                       if((i) % 100 == 0){     pDataArray->m->mothurOut(toString(i)); pDataArray->m->mothurOutEndLine();               }\r
+                       if((i) % 100 == 0){     pDataArray->m->mothurOutJustToScreen(toString(i)+"\n");                 }\r
                }\r
                \r
-        if((pDataArray->count) % 100 != 0){    pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();               }\r
+        if((pDataArray->count) % 100 != 0){    pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count)+"\n");                 }\r
         \r
                in.close();\r
         out.close();\r