Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / clustalw / src / fileInput / InFileStream.cpp

diff --git a/website/archive/binaries/mac/src/clustalw/src/fileInput/InFileStream.cpp b/website/archive/binaries/mac/src/clustalw/src/fileInput/InFileStream.cpp
new file mode 100644 (file)
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+++ b/website/archive/binaries/mac/src/clustalw/src/fileInput/InFileStream.cpp
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+/**
+ * Author: Nigel Brown
+ * 
+ * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
+ */
+/**
+ * InFileStream subclasses std::ifstream, adding a check for the end-of-line
+ * character convention in the input file. This is then used by the getline()
+ * member as the line delimiter, unless the caller supplies an explicit
+ * delimiter.
+ *
+ * Note: This is an ugly workaround; at present various operations repeatedly
+ * construct/destruct an instance and open/close a sequence file up to 12
+ * times! A cleaner class will probably derive this class from something like
+ * 'istream' aggregating a 'filebuf' under control of istream::seekg().
+ *
+ * Created: 09-02-07,Nigel Brown(EMBL)
+ * 
+ * Changes:
+ * Mark Larkin 13-2-07: I removed the dynamic cast from the getline functions. 
+ ***************************************************************************/
+#ifdef HAVE_CONFIG_H
+    #include "config.h"
+#endif
+#include <string>
+#include <fstream>
+#include <iostream>
+#include "InFileStream.h"
+using namespace std;
+
+const char LF = 0x0a;  //linefeed
+const char CR = 0x0d;  //carriage return
+
+InFileStream::InFileStream() :
+    ifstream()
+{
+    delim = '\n'; // default
+    //cout << "InFileStream() constructor 1" << endl;
+}
+
+InFileStream::InFileStream(const char *filename) :
+    ifstream(filename, ios::in), filename(filename)
+{
+    //cout << "InFileStream(f) constructor 2" << endl;
+    delim = findDelimiter();
+}
+
+//- copy-constructor: can't copy superclass private members
+//- InFileStream::InFileStream(const InFileStream &copy) :
+//-     ifstream(static_cast<const ifstream&>(copy))
+//- {
+//-     cout << "InFileStream() constructor 3" << endl;
+//-     delim = copy.delim;
+//- }
+
+void InFileStream::open(const char *filename) 
+{
+
+    this->filename = filename;
+    ifstream::open(filename, ios::in);
+    if  (ifstream::fail())
+        return;
+    delim = findDelimiter();
+}
+
+//not necessary, but for symmetry to open()
+void InFileStream::close() 
+{
+    ifstream::close();   
+}
+
+
+//getline with stored delimiter
+std::istream& InFileStream::getline(char *s, streamsize n) 
+{
+    return ifstream::getline(s, n, delim);
+}
+
+//getline with caller supplied delimiter
+std::istream& InFileStream::getline(char *s, streamsize n, char delim) 
+{
+    return ifstream::getline(s, n, delim);
+}
+
+
+/**
+ * Mark 24-1-2007. I added the function findDelimiter to determine if '\r' or
+ * '\n' will be used as the line delimiter when parsing the file.
+ *
+ * 25-01-07,Nigel Brown(EMBL): changed body of loop to check successive chars
+ * in case of DOS/Windows
+ *
+ * 09-02-07,Nigel Brown(EMBL): moved member into new InFileStream subclassed
+ * from std::ifstream, so this is called automatically for any file reader
+ * that uses InFileStream in place of std::ifstream. Replaced if/then/else
+ * with switch.
+ */
+char InFileStream::findDelimiter()
+{
+    ifstream in;
+    int type = 0;
+    
+    in.open(filename.c_str(), ios::in);
+    if (in.fail())
+        return delim;
+    
+    in.seekg(0, ios::beg);
+
+    //look for CR or LF or CRLF (or LFCR)
+    if (in.is_open()) {
+        char c;
+        while (in.get(c)) {
+            if (c == CR)
+                type |= 1;
+            else if (c == LF)
+                type |= 2;
+            else if (type)
+                break;
+        }
+    }
+    in.close();
+
+    switch (type) {
+       case 1:
+           //cout << "file is Mac System 9" << endl;
+           delim = '\r';
+           break;
+       case 2:
+           //cout << "file is UNIX" << endl;
+           delim = '\n';
+           break;
+       case 3:
+           //cout << "file is DOS" << endl;
+           delim = '\n';
+           break;
+       default: //short or empty file
+           //cout << "file is UNIX (default)" << endl;
+           delim = '\n';
+    }
+    return delim;
+}
+
+