Remove gzstream

CMakeLists.txt

@@ -214,7 +214,6 @@ include_directories(lib/simde)
 
 include_directories(lib)
 include_directories(lib/simd)
-include_directories(lib/gzstream)
 include_directories(lib/alp)
 include_directories(lib/cacode)
 include_directories(lib/ksw2)

src/commons/GzReader.h

@@ -0,0 +1,93 @@
+#include "Debug.h"
+
+#include <cstdio>
+#include <string>
+#include <cstring>
+
+#ifdef HAVE_ZLIB
+#include <zlib.h>
+#endif
+
+class GzReader {
+public:
+    enum Mode {
+        FILE_MODE,
+#ifdef HAVE_ZLIB
+        GZ_MODE
+#endif
+    };
+
+    GzReader(const std::string &filename) {
+        if (filename.size() >= 3 && filename.substr(filename.size() - 3) == ".gz") {
+#ifdef HAVE_ZLIB
+            mode = GZ_MODE;
+            gzHandle = gzopen(filename.c_str(), "r");
+            openFailed = !gzHandle;
+            return;
+#else
+            Debug(Debug::ERROR) << "MMseqs2 was not compiled with zlib support. Cannot read compressed input\n";
+            EXIT(EXIT_FAILURE);
+#endif
+        }
+        mode = FILE_MODE;
+        file = fopen(filename.c_str(), "r");
+        openFailed = !file;
+    }
+
+    ~GzReader() {
+        if (mode == FILE_MODE && file) fclose(file);
+#ifdef HAVE_ZLIB
+        else if (mode == GZ_MODE && gzHandle) gzclose(gzHandle);
+#endif
+    }
+
+    bool fail() const {
+        return openFailed;
+    }
+
+    bool getline(std::string &line) {
+        line.clear();
+        if (openFailed) return false;
+
+        char buffer[4096];
+        bool complete = false;
+        while (!complete) {
+            if (mode == FILE_MODE) {
+                if (fgets(buffer, sizeof(buffer), file) != NULL) {
+                    if (char *newline = strchr(buffer, '\n')) {
+                        line.append(buffer, newline - buffer);
+                        complete = true;
+                    } else {
+                        line.append(buffer);
+                    }
+                } else {
+                    return !line.empty();
+                }
+            }
+    #ifdef HAVE_ZLIB
+            else if (mode == GZ_MODE) {
+                if (gzgets(gzHandle, buffer, sizeof(buffer)) != NULL) {
+                    if (char *newline = strchr(buffer, '\n')) {
+                        line.append(buffer, newline - buffer);
+                        complete = true;
+                    } else {
+                        line.append(buffer);
+                    }
+                } else {
+                    return !line.empty();
+                }
+            }
+    #endif
+        }
+
+        return true;
+    }
+
+private:
+    Mode mode;
+    bool openFailed = false;
+    FILE *file = NULL;
+#ifdef HAVE_ZLIB
+    gzFile gzHandle = NULL;
+#endif
+};

src/util/convertkb.cpp

@@ -4,10 +4,7 @@
 #include "FileUtil.h"
 #include "Debug.h"
 #include "UniprotKB.h"
-
-#ifdef HAVE_ZLIB
-#include "gzstream.h"
-#endif
+#include "GzReader.h"
 
 #include <fstream>
 #include <set>
@@ -102,27 +99,16 @@ int convertkb(int argc, const char **argv, const Command &command) {
 
     Debug::Progress progress;
     for (std::vector<std::string>::const_iterator it = par.filenames.begin(); it != par.filenames.end(); ++it) {
-        std::istream *kbIn;
-        if (Util::endsWith(".gz", *it)) {
-#ifdef HAVE_ZLIB
-            kbIn = new igzstream((*it).c_str());
-#else
-            Debug(Debug::ERROR) << "MMseqs2 was not compiled with zlib support. Can not read compressed input\n";
-            EXIT(EXIT_FAILURE);
-#endif
-        } else {
-            kbIn = new std::ifstream(*it);
-        }
-
-        if (kbIn->fail()) {
+        GzReader kbIn(*it);
+        if (kbIn.fail()) {
             Debug(Debug::ERROR) << "File " << (*it) << " not found\n";
             EXIT(EXIT_FAILURE);
         }
 
         Debug(Debug::INFO) << "Extracting data from " << (*it) << "\n";
         std::string line;
         unsigned int i = 0;
-        while (std::getline(*kbIn, line)) {
+        while (kbIn.getline(line)) {
             if (line.length() < 2) {
                 Debug(Debug::WARNING) << "Invalid entry\n";
                 continue;
@@ -156,7 +142,6 @@ int convertkb(int argc, const char **argv, const Command &command) {
                 i++;
             }
         }
-        delete kbIn;
     }
 
     for (std::vector<unsigned int>::const_iterator it = enabledColumns.begin(); it != enabledColumns.end(); ++it) {