Add BLAST_QC_C and BLAST_QC_JAVA versions. Update BLAST-QC.py

torkian · May 27, 2020 · 3d46ed4 · 3d46ed4
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diff --git a/BLAST-QC.py b/BLAST-QC.py
diff --git a/BLAST_QC_C/.DS_Store b/BLAST_QC_C/.DS_Store
diff --git a/BLAST_QC_C/BLASTQC b/BLAST_QC_C/BLASTQC
diff --git a/BLAST_QC_C/BLASTQC.c b/BLAST_QC_C/BLASTQC.c
diff --git a/BLAST_QC_C/BLASTQC.h b/BLAST_QC_C/BLASTQC.h
@@ -0,0 +1,23 @@
+#ifndef _BLAST_QC_H_
+#define _BLAST_QC_H_
+#include <limits.h>
+
+//  BLAST_QC ARGS :
+char FILENAME[100] = "out.xml"; 
+char FILEFORMAT[100] = "XML";
+char OUTFILE[100] = "";
+char TYPE = 'p';
+int NUMBER = -1;
+double EVALUE = -1;
+double BITSCORE = -1;
+double IDENTITY = -1;
+int DEFINITION = -1;
+char ORDER = '\0';
+double ERANGE = -1;
+double BRANGE = -1;
+double IRANGE = -1;
+//
+#define BUFFER_SIZE 1024
+
+
+#endif  
diff --git a/BLAST_QC_C/libxml2/libxml/DOCBparser.h b/BLAST_QC_C/libxml2/libxml/DOCBparser.h
@@ -0,0 +1,109 @@
+/*
+ * Summary: old DocBook SGML parser
+ * Description: interface for a DocBook SGML non-verifying parser
+ * This code is DEPRECATED, and should not be used anymore.
+ *
+ * Copy: See Copyright for the status of this software.
+ *
+ * Author: Daniel Veillard
+ */
+
+#ifndef __DOCB_PARSER_H__
+#define __DOCB_PARSER_H__
+#include <libxml/xmlversion.h>
+
+#ifdef LIBXML_DOCB_ENABLED
+
+#include <libxml/parser.h>
+#include <libxml/parserInternals.h>
+
+#ifndef IN_LIBXML
+#ifdef __GNUC__
+#warning "The DOCBparser module has been deprecated in libxml2-2.6.0"
+#endif
+#endif
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#if defined(_WIN32)
+#define LIBXML2_DOCB_DEPRECATED
+#else
+#include <Availability.h>
+#include <TargetConditionals.h>
+#define LIBXML2_DOCB_DEPRECATED __OSX_DEPRECATED(10.4, 10.4, "Deprecated in libxml2 v2.6.0") \
+                                __IOS_DEPRECATED(2.0, 2.0, "Deprecated in libxml2 v2.6.0") \
+                                __TVOS_DEPRECATED(9.0, 9.0, "Deprecated in libxml2 v2.6.0") \
+                                __WATCHOS_DEPRECATED(1.0, 1.0, "Deprecated in libxml2 v2.6.0")
+#endif
+
+/*
+ * Most of the back-end structures from XML and SGML are shared.
+ */
+typedef xmlParserCtxt docbParserCtxt;
+typedef xmlParserCtxtPtr docbParserCtxtPtr;
+typedef xmlSAXHandler docbSAXHandler;
+typedef xmlSAXHandlerPtr docbSAXHandlerPtr;
+typedef xmlParserInput docbParserInput;
+typedef xmlParserInputPtr docbParserInputPtr;
+typedef xmlDocPtr docbDocPtr;
+
+/*
+ * There is only few public functions.
+ */
+XMLPUBFUN int XMLCALL
+		     docbEncodeEntities(unsigned char *out,
+                                        int *outlen,
+                                        const unsigned char *in,
+                                        int *inlen, int quoteChar) LIBXML2_DOCB_DEPRECATED;
+
+XMLPUBFUN docbDocPtr XMLCALL
+		     docbSAXParseDoc   (xmlChar *cur,
+                                        const char *encoding,
+                                        docbSAXHandlerPtr sax,
+                                        void *userData) LIBXML2_DOCB_DEPRECATED;
+XMLPUBFUN docbDocPtr XMLCALL
+		     docbParseDoc      (xmlChar *cur,
+                                        const char *encoding) LIBXML2_DOCB_DEPRECATED;
+XMLPUBFUN docbDocPtr XMLCALL
+		     docbSAXParseFile  (const char *filename,
+                                        const char *encoding,
+                                        docbSAXHandlerPtr sax,
+                                        void *userData) LIBXML2_DOCB_DEPRECATED;
+XMLPUBFUN docbDocPtr XMLCALL
+		     docbParseFile     (const char *filename,
+                                        const char *encoding) LIBXML2_DOCB_DEPRECATED;
+
+/**
+ * Interfaces for the Push mode.
+ */
+XMLPUBFUN void XMLCALL
+		     docbFreeParserCtxt      (docbParserCtxtPtr ctxt) LIBXML2_DOCB_DEPRECATED;
+XMLPUBFUN docbParserCtxtPtr XMLCALL
+		     docbCreatePushParserCtxt(docbSAXHandlerPtr sax,
+                                              void *user_data,
+                                              const char *chunk,
+                                              int size,
+                                              const char *filename,
+                                              xmlCharEncoding enc) LIBXML2_DOCB_DEPRECATED;
+XMLPUBFUN int XMLCALL
+		     docbParseChunk          (docbParserCtxtPtr ctxt,
+                                              const char *chunk,
+                                              int size,
+                                              int terminate) LIBXML2_DOCB_DEPRECATED;
+XMLPUBFUN docbParserCtxtPtr XMLCALL
+		     docbCreateFileParserCtxt(const char *filename,
+                                              const char *encoding) LIBXML2_DOCB_DEPRECATED;
+XMLPUBFUN int XMLCALL
+		     docbParseDocument       (docbParserCtxtPtr ctxt) LIBXML2_DOCB_DEPRECATED;
+
+#undef LIBXML2_DOCB_DEPRECATED
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* LIBXML_DOCB_ENABLED */
+
+#endif /* __DOCB_PARSER_H__ */