--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/include/gfile.c	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,430 @@
+/******************************************************************************
+** @source GEMBASSY file routines
+**
+** @version 1.0
+** @modified December 27 2012 Hidetoshi Itaya Created this file
+** @@
+**
+** This library is free software; you can redistribute it and/or
+** modify it under the terms of the GNU Library General Public
+** License as published by the Free Software Foundation; either
+** version 2 of the License, or (at your option) any later version.
+**
+** This library is distributed in the hope that it will be useful,
+** but WITHOUT ANY WARRANTY; without even the implied warranty of
+** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+** Library General Public License for more details.
+**
+** You should have received a copy of the GNU Library General Public
+** License along with this library; if not, write to the
+** Free Software Foundation, Inc., 59 Temple Place - Suite 330,
+** Boston, MA  02111-1307, USA.
+******************************************************************************/
+
+#include "gfile.h"
+
+
+
+
+/* @func gValID ***************************************************************
+**
+** Checks if an input string is a valid ID
+**
+** @param id [r]  [AjPStr] ID to check
+** @return [AjBool]
+** @@
+******************************************************************************/
+
+ajint gValID(AjPStr id){
+  AjPFilebuff buff = NULL;
+  AjPStr      url  = NULL;
+  AjPStr      line = NULL;
+  AjPRegexp   pval = NULL;
+
+  url = ajStrNewC("http://web.sfc.keio.ac.jp/~t11080hi/valID/valID.cgi?id=");
+  url = ajStrNew();
+  ajFmtPrintS(&url, "http://rest.g-language.org/%S", id);
+
+  //ajStrAppendS(&url, id);
+
+  if(!gFilebuffURLS(url, &buff)) {
+    return ajFalse;
+  }
+
+  return ajTrue;
+
+  ajBuffreadLine(buff, &line);
+
+  pval = ajRegCompC("^0");
+
+  if(ajRegExec(pval, line))
+    return ajFalse;
+
+  return ajTrue;
+}
+
+
+
+
+/* @func gStrAppendURLS *******************************************************
+**
+** Downloads file from a specified URL and writes to given output file
+**
+** @param [r] url [AjPStr] URL to download file from
+** @param [r] string [AjPStr] String to write into
+** @return [AjBool] 
+** @@
+******************************************************************************/
+
+AjBool gStrAppendURLS(AjPStr url, AjPStr* string){
+  AjPFilebuff buff = NULL;
+  AjPStr      file = NULL;
+  AjPStr      line = NULL;
+
+  if(!*string)
+    *string = ajStrNew();
+
+  if(!gFilebuffURLS(url, &buff))
+    return ajFalse;
+
+  while(ajBuffreadLine(buff, &line)){
+    ajStrAppendS(string, line);
+  }
+
+  ajFilebuffDel(&buff);
+
+  return ajTrue;
+}
+
+
+
+
+/* @func gStrAppendURLC *******************************************************
+**
+** Downloads file from a specified URL and writes to given output file
+**
+** @param [r] url [char*] URL to download file from
+** @param [r] string [AjPStr] String to write into
+** @return [AjBool] 
+** @@
+******************************************************************************/
+
+AjBool gStrAppendURLC(char* url, AjPStr* string){
+  if(!gStrAppendURLS(ajStrNewC(url), string))
+    {
+      return ajFalse;
+    }
+
+  return ajTrue;
+}
+
+
+
+
+/* @func gFileOutURLS *********************************************************
+**
+** Downloads file from a specified URL and writes to given output file
+**
+** @param [r] url [AjPStr] URL to download file from
+** @param [r] outf [AjPFile] File object to write into
+** @return [AjBool] 
+** @@
+******************************************************************************/
+
+AjBool gFileOutURLS(AjPStr url, AjPFile* outf){
+  AjPFilebuff buff = NULL;
+  AjPStr      file = NULL;
+  AjPStr      line = NULL;
+
+  if(!gFilebuffURLS(url, &buff))
+    return ajFalse;
+
+  while(ajBuffreadLine(buff, &line)){
+    ajWriteline(*outf, line);
+  }
+
+  ajFilebuffDel(&buff);
+
+  return ajTrue;
+}
+
+
+
+
+/* @func gFileOutURLC *********************************************************
+**
+** Downloads file from a specified URL and writes to given output file
+**
+** @param [r] url [char*] URL to download file from
+** @param [r] outf [AjPFile] File object to write into
+** @return [AjBool] 
+** @@
+******************************************************************************/
+
+AjBool gFileOutURLC(char* url, AjPFile* outf){
+  if(!gFileOutURLS(ajStrNewC(url), outf))
+    {
+      return ajFalse;
+    }
+
+  return ajTrue;
+}
+
+
+
+
+/* @func gFilebuffURLS ********************************************************
+**
+** Downloads file from a specified URL and inputs in file buffer
+**
+** @param [r] url [AjPStr] URL to download file from
+** @param [r] buff [AjPFilebuff] File buffer to set
+** @return [AjBool]
+** @@
+******************************************************************************/
+
+AjBool gFilebuffURLS(AjPStr url, AjPFilebuff* buff){
+  AjPStr line = NULL;
+  AjPStr host = NULL;
+  AjPStr path = NULL;
+  ajint  port = 80;
+
+  ajHttpUrlDeconstruct(url, &port, &host, &path);
+
+  *buff = ajHttpRead(NULL, NULL, NULL, host, port, path);
+
+  if(!*buff)
+    return ajFalse;
+
+  ajFilebuffHtmlNoheader(*buff);
+
+  return ajTrue;
+}
+
+
+
+
+/* @func gFilebuffURLC ********************************************************
+**
+** Downloads file from a specified URL and inputs in file buffer
+**
+** @param [r] url [char*] URL to download file from
+** @param [r] buff [AjPFilebuff] File buffer to set
+** @return [AjBool]
+** @@
+******************************************************************************/
+
+AjBool gFilebuffURLC(char* url, AjPFilebuff* buff){
+  gFilebuffURLS(ajStrNewC(url), buff);
+
+  if(!*buff)
+    return ajFalse;
+
+  return ajTrue;
+}
+
+
+
+
+/* @func gAssignUniqueName ****************************************************
+**
+** Creates a unique filename
+**
+** @return [AjPStr] the unique filename
+** @@
+******************************************************************************/
+
+void gAssignUniqueName(AjPStr *string) {
+  static char ext[2] = "A";
+
+  ajFmtPrintS(string, "%08d%s", getpid(), ext);
+
+  if( ++ext[0] > 'Z' ) {
+    ext[0] = 'A';
+  }
+}
+
+
+
+
+/* @func gCreateUniqueName ****************************************************
+**
+** Returns a unique filename
+**
+** @return [AjPStr] the unique filename
+** @@
+******************************************************************************/
+
+AjPStr gCreateUniqueName() {
+  AjPStr string;
+
+  gAssignUniqueName(&string);
+
+  return string;
+}
+
+
+
+
+/* @func gFormatGenbank *******************************************************
+**
+** Creates a genbank format string with sequence and features
+**
+** @param [r] seq [AjPSeq] Sequence object to write
+** @param [r] inseq [AjPStr] String to write to
+** @return [AjBool]
+** @@
+******************************************************************************/
+
+AjBool gFormatGenbank(AjPSeq seq, AjPStr *inseq){
+  AjPSeqout     seqout   = NULL;
+  AjPFeattabOut featout  = NULL;
+  AjPFeattable  feat     = NULL;
+  AjPStr        seqline  = NULL;
+  AjPStr        featline = NULL;
+  AjPFile       seqfile  = NULL;
+  AjPFile       featfile = NULL;
+  AjPStr        filename = NULL;
+  AjBool        hasfeats = ajTrue;
+
+  gAssignUniqueName(&filename);
+  feat = ajSeqGetFeatCopy(seq);
+
+  if(!feat) {
+    hasfeats = ajFalse;
+  }
+
+  seqout = ajSeqoutNew();
+
+  if(!ajSeqoutOpenFilename(seqout,filename))
+    embExitBad();
+
+  ajSeqoutSetFormatS(seqout,ajStrNewC("genbank"));
+  ajSeqoutWriteSeq(seqout,seq);
+  ajSeqoutClose(seqout);
+  ajSeqoutDel(&seqout);
+
+  seqfile = ajFileNewInNameS(filename);
+  ajSysFileUnlinkS(filename);
+
+  if(hasfeats) {
+    featout = ajFeattabOutNew();
+
+    if(!ajFeattabOutOpen(featout,filename))
+      return ajFalse;
+
+    ajFeattableWriteGenbank(featout,feat);
+
+    ajFeattableDel(&feat);
+    //ajFeattabOutDel(&featout);
+    ajFileClose(&(featout->Handle));
+
+    featfile = ajFileNewInNameS(filename);
+    ajSysFileUnlinkS(filename);
+  }
+
+  while(ajReadline(seqfile,&seqline)){
+    if(hasfeats && ajStrMatchC(seqline,"ORIGIN\n")){
+      while(ajReadline(featfile,&featline)){
+        ajStrAppendS(inseq, featline);
+      }
+    }
+    ajStrAppendS(inseq, seqline);
+  }
+
+  ajStrDel(&seqline);
+  ajStrDel(&featline);
+  ajStrDel(&filename);
+  ajFileClose(&seqfile);
+  ajFileClose(&featfile);
+
+  return hasfeats;
+}
+
+
+
+
+/* @func gGetFileContent ******************************************************
+**
+** Reads file content and sets it to string pointer
+**
+** @param [r] content [AjPSeq] String to write to
+** @param [r] filename [AjPSeq] Filename to open
+** @return [AjBool]
+** @@
+******************************************************************************/
+
+AjBool gGetFileContent(AjPStr* content, AjPStr filename){
+  AjPFile file    = NULL;
+  AjPStr  line    = NULL;
+
+  if((file = ajFileNewInNameS(filename)) == NULL)
+    return ajFalse;
+
+  while(ajReadline(file, &line))
+    ajStrAppendS(content, line);
+
+  if(file)
+    ajFileClose(&file);
+
+  ajSysFileUnlinkS(filename);
+
+  return ajTrue;
+}
+
+
+
+
+/* @func gtaiFileOutURLS ******************************************************
+**
+** Downloads file from a specified URL and inputs in file buffer
+**
+** @param [r] url [AjPStr] URL to download file from
+** @param [r] buff [AjPFilebuff] File buffer to set
+** @return [AjBool]
+** @@
+******************************************************************************/
+
+AjBool gtaiFileOutURLS(AjPStr url, AjPFile* outf, AjBool tai){
+  if(tai)
+    {
+      CURL *curl;
+      CURLcode curl_res;
+
+      Memory *mem = malloc(sizeof(Memory*));
+
+      mem->size = 0;
+      mem->memory = NULL;
+
+      curl_global_init(CURL_GLOBAL_ALL);
+
+      curl = curl_easy_init();
+
+      if(curl)
+        {
+          curl_easy_setopt(curl, CURLOPT_URL, ajCharNewS(url));
+          curl_easy_setopt(curl, CURLOPT_FOLLOWLOCATION, 1);
+          curl_easy_setopt(curl, CURLOPT_WRITEFUNCTION, curl_write);
+          curl_easy_setopt(curl, CURLOPT_WRITEDATA, mem);
+        }
+
+      curl_res = curl_easy_perform(curl);
+
+      if(CURLE_OK == curl_res)
+        {
+          char* redir;
+          curl_res = curl_easy_getinfo(curl, CURLINFO_EFFECTIVE_URL, &redir);
+
+          if((CURLE_OK == curl_res) && redir) {
+            ajStrAssignC(&url, redir);
+            ajStrExchangeCC(&url, "cai.csv", "tai.csv");
+          }
+        }
+
+      free(mem);
+      curl_easy_cleanup(curl);
+      curl_global_cleanup();
+    }
+
+  return gFileOutURLS(url, outf);
+}