Refactor the parsers for better compatibility and memory usage

include/FormatHandling/BaseFormatHandler.h

@@ -32,6 +32,7 @@
 
 #include "Alignment/Alignment.h"
 #include "reportsystem.h"
+#include "utils.h"
 
 #include <iomanip>
 
@@ -90,7 +91,37 @@ class BaseFormatHandler {
      \return    <b> Alignment</b> loaded with the information of the file. \n
                 <b> nullptr</b> if there was any error.
      */
-    virtual Alignment *LoadAlignment(const std::string &filename) = 0;
+    virtual Alignment *LoadAlignment(const std::string &filename) {
+        Alignment* alignment;
+        std::ifstream file;
+
+        file.open(filename, std::ifstream::in);
+        if(!utils::checkFile(file))
+            return nullptr;
+
+        alignment = LoadAlignment(file);
+        if (alignment != nullptr) {
+            /* Alignment title may be set by the format handler, dependending on 
+             * the alignment format, so it should only be set here if there was
+             * none parsed already.
+             */
+            if (alignment->filename.empty()) {
+                alignment->filename.append(filename);
+                alignment->filename.append(";");
+            }
+        }
+
+        file.close();
+        return alignment;
+    }
+
+    /**
+     \brief Function to load a file in the current format and return an alignment object.
+     \param filename Filename of the file to load.
+     \return    <b> Alignment</b> loaded with the information of the file. \n
+                <b> nullptr</b> if there was any error.
+     */
+    virtual Alignment *LoadAlignment(std::istream &file) = 0;
 
     /**
      \brief Function to save a \link Alignment \endlink to a file.

include/FormatHandling/clustal_state.h

@@ -45,7 +45,7 @@ class clustal_state : public BaseFormatHandler {
 
     int CheckAlignment(std::istream *origin) override;
 
-    Alignment *LoadAlignment(const std::string &filename) override;
+    Alignment *LoadAlignment(std::istream& stream) override;
 
     bool SaveAlignment(const Alignment &alignment, std::ostream *output) override;
 

include/FormatHandling/fasta_m10_state.h

@@ -46,7 +46,7 @@ class fasta_m10_state : public BaseFormatHandler {
 
     int CheckAlignment(std::istream *origin) override;
 
-    Alignment *LoadAlignment(const std::string &filename) override;
+    Alignment *LoadAlignment(std::istream& stream) override;
 
     bool SaveAlignment(const Alignment &alignment, std::ostream *output) override;
 

include/FormatHandling/fasta_state.h

@@ -46,7 +46,7 @@ class fasta_state : public BaseFormatHandler {
 
     int CheckAlignment(std::istream *origin) override;
 
-    Alignment *LoadAlignment(const std::string &filename) override;
+    Alignment *LoadAlignment(std::istream& stream) override;
 
     bool SaveAlignment(const Alignment &alignment, std::ostream *output) override;
 

include/FormatHandling/htmlreport_state.h

@@ -46,7 +46,7 @@ class htmlreport_state : public BaseFormatHandler {
 
     int CheckAlignment(std::istream *origin) override;
 
-    Alignment *LoadAlignment(const std::string &filename) override;
+    Alignment *LoadAlignment(std::istream& stream) override;
 
     bool SaveAlignment(const Alignment &alignment, std::ostream *output) override;
 

include/FormatHandling/mega_interleaved_state.h

@@ -46,7 +46,7 @@ class mega_interleaved_state : public BaseFormatHandler {
 
     int CheckAlignment(std::istream *origin) override;
 
-    Alignment *LoadAlignment(const std::string &filename) override;
+    Alignment *LoadAlignment(std::istream& stream) override;
 
     bool SaveAlignment(const Alignment &alignment, std::ostream *output) override;
 

include/FormatHandling/mega_sequential_state.h

@@ -46,7 +46,7 @@ class mega_sequential_state : public BaseFormatHandler {
 
     int CheckAlignment(std::istream *origin) override;
 
-    Alignment *LoadAlignment(const std::string &filename) override;
+    Alignment *LoadAlignment(std::istream& stream) override;
 
     bool SaveAlignment(const Alignment &alignment, std::ostream *output) override;
 

include/FormatHandling/nexus_m10_state.h

@@ -46,7 +46,7 @@ class nexus_m10_state : public BaseFormatHandler {
 
     int CheckAlignment(std::istream *origin) override;
 
-    Alignment *LoadAlignment(const std::string &filename) override;
+    Alignment *LoadAlignment(std::istream& stream) override;
 
     bool SaveAlignment(const Alignment &alignment, std::ostream *output) override;
 

include/FormatHandling/nexus_state.h

@@ -46,7 +46,7 @@ class nexus_state : public BaseFormatHandler {
 
     int CheckAlignment(std::istream *origin) override;
 
-    Alignment *LoadAlignment(const std::string &filename) override;
+    Alignment *LoadAlignment(std::istream& stream) override;
 
     bool SaveAlignment(const Alignment &alignment, std::ostream *output) override;
 

include/FormatHandling/phylip32_m10_state.h

@@ -46,7 +46,7 @@ class phylip32_m10_state : public BaseFormatHandler {
 
     int CheckAlignment(std::istream *origin) override;
 
-    Alignment *LoadAlignment(const std::string &filename) override;
+    Alignment *LoadAlignment(std::istream& stream) override;
 
     bool SaveAlignment(const Alignment &alignment, std::ostream *output) override;
 

include/FormatHandling/phylip32_state.h

@@ -46,7 +46,7 @@ class phylip32_state : public BaseFormatHandler {
 
     int CheckAlignment(std::istream *origin) override;
 
-    Alignment *LoadAlignment(const std::string &filename) override;
+    Alignment *LoadAlignment(std::istream& stream) override;
 
     bool SaveAlignment(const Alignment &alignment, std::ostream *output) override;
 

include/FormatHandling/phylip40_m10_state.h

@@ -46,7 +46,7 @@ class phylip40_m10_state : public BaseFormatHandler {
 
     int CheckAlignment(std::istream *origin) override;
 
-    Alignment *LoadAlignment(const std::string &filename) override;
+    Alignment *LoadAlignment(std::istream& stream) override;
 
     bool SaveAlignment(const Alignment &alignment, std::ostream *output) override;
 

include/FormatHandling/phylip40_state.h

@@ -46,7 +46,7 @@ class phylip40_state : public BaseFormatHandler {
 
     int CheckAlignment(std::istream *origin) override;
 
-    Alignment *LoadAlignment(const std::string &filename) override;
+    Alignment *LoadAlignment(std::istream& stream) override;
 
     bool SaveAlignment(const Alignment &alignment, std::ostream *output) override;
 

include/FormatHandling/phylip_paml_m10_state.h

@@ -46,7 +46,7 @@ class phylip_paml_m10_state : public BaseFormatHandler {
 
     int CheckAlignment(std::istream *origin) override;
 
-    Alignment *LoadAlignment(const std::string &filename) override;
+    Alignment *LoadAlignment(std::istream& stream) override;
 
     bool SaveAlignment(const Alignment &alignment, std::ostream *output) override;
 

include/FormatHandling/phylip_paml_state.h

@@ -46,7 +46,7 @@ class phylip_paml_state : public BaseFormatHandler {
 
     int CheckAlignment(std::istream *origin) override;
 
-    Alignment *LoadAlignment(const std::string &filename) override;
+    Alignment *LoadAlignment(std::istream& stream) override;
 
     bool SaveAlignment(const Alignment &alignment, std::ostream *output) override;
 

include/FormatHandling/pir_state.h

@@ -46,7 +46,7 @@ class pir_state : public BaseFormatHandler {
 
     int CheckAlignment(std::istream *origin) override;
 
-    Alignment *LoadAlignment(const std::string &filename) override;
+    Alignment *LoadAlignment(std::istream& stream) override;
 
     bool SaveAlignment(const Alignment &alignment, std::ostream *output) override;
 

include/utils.h

@@ -254,19 +254,6 @@ namespace utils {
      */
      bool checkFile(std::ifstream &file);
 
-    /**
-     \brief Read a new line from current input stream.\n
-     This function is better than standard one
-      since cares of operative system compatibility.\n
-     It is useful as well because removes tabs and blank spaces
-      at lines at beginning/ending.\n
-     \param file ifstream to read line from.
-     \return \n
-        Line that has been read or
-        nullptr if there is nothing to read.\n
-     */
-     char *readLine(std::ifstream &file);
-
     /**
      \brief Read a new line from current input stream.\n
      This function is better than standard one
@@ -278,7 +265,7 @@ namespace utils {
       nullptr if there is nothing to read.\n
       Line that has been read.
     */
-     char *readLine(std::istream &file);
+     char *readLine(std::istream &file, std::string &buffer);
 
     /**
      \brief Remove all content surrounded by ("") or ([]).\n

source/FormatHandling/clustal_state.cpp

@@ -39,18 +39,16 @@ int clustal_state::CheckAlignment(std::istream* origin)
     origin->seekg(0);
     origin->clear();
     char *firstWord = nullptr, *line = nullptr;
-
+    std::string buffer;
 
     /* Read first valid line in a safer way */
     do {
-        delete[] line;
-        line = utils::readLine(*origin);
+        line = utils::readLine(*origin, buffer);
     } while ((line == nullptr) && (!origin->eof()));
 
     /* If the file end is reached without a valid line, warn about it */
     if (origin->eof())
     {
-        delete [] line;
         return false;
     }
 
@@ -60,33 +58,22 @@ int clustal_state::CheckAlignment(std::istream* origin)
     /* Clustal Format */
     if((!strcmp(firstWord, "CLUSTAL")) || (!strcmp(firstWord, "clustal")))
     {
-        delete [] line;
         return 1;
     }
-
-    delete[] line;
 
     return 0;
 }
 
-Alignment* clustal_state::LoadAlignment(const std::string &filename)
+Alignment* clustal_state::LoadAlignment(std::istream &file)
 {
     Alignment* alignment = new Alignment();
     int i, seqLength, pos, firstBlock;
     char *str, *line = nullptr;
-    std::ifstream file;
-    file.open(filename, std::ifstream::in);
-
-    /* Store some details about input file to be used in posterior format
-     * conversions */
-    // alignment.filename.append("!Title ");
-    alignment->filename.append(filename);
-    alignment->filename.append(";");
+    std::string buffer;
 
     /* The first valid line corresponding to CLUSTAL label is ignored */
     do {
-        delete [] line;
-        line = utils::readLine(file);
+        line = utils::readLine(file, buffer);
     } while ((line == nullptr) && (!file.eof()));
 
     /* If the file end is reached without a valid line, warn about it */
@@ -95,12 +82,8 @@ Alignment* clustal_state::LoadAlignment(const std::string &filename)
 
     /* Ignore blank lines before first sequence block starts */
     while(!file.eof()) {
-
-        /* Deallocate previously used dynamic memory */
-        delete [] line;
-
         /* Read lines in safe way */
-        line = utils::readLine(file);
+        line = utils::readLine(file, buffer);
 
         if (line != nullptr)
             break;
@@ -130,15 +113,10 @@ Alignment* clustal_state::LoadAlignment(const std::string &filename)
             break;
         alignment->numberOfSequences++;
 
-        /* Deallocate previously used dynamic memory */
-        delete [] line;
-
         /* Read lines in safe way */
-        line = utils::readLine(file);
+        line = utils::readLine(file, buffer);
     }
 
-    delete [] line;
-
     /* Finish to preprocess the input file. */
     file.clear();
     file.seekg(0);
@@ -148,19 +126,16 @@ Alignment* clustal_state::LoadAlignment(const std::string &filename)
     alignment->sequences = new std::string[alignment->numberOfSequences];
 
     /* Read the title line and store it */
-    line = utils::readLine(file);
+    line = utils::readLine(file, buffer);
     if (line == nullptr)
         return nullptr;
     alignment->alignmentInfo.append(line, strlen(line));
 
     /* Ignore blank lines before first sequence block starts */
     while(!file.eof()) {
 
-        /* Deallocate previously used dynamic memory */
-        delete [] line;
-
         /* Read lines in safe way */
-        line = utils::readLine(file);
+        line = utils::readLine(file, buffer);
 
         if (line != nullptr)
             break;
@@ -181,7 +156,7 @@ Alignment* clustal_state::LoadAlignment(const std::string &filename)
             if (i == 0)
                 firstBlock = false;
             /* Read current line and analyze it*/
-            line = utils::readLine(file);
+            line = utils::readLine(file, buffer);
             continue;
         }
 
@@ -196,11 +171,8 @@ Alignment* clustal_state::LoadAlignment(const std::string &filename)
         if (pos == seqLength) {
             firstBlock = false;
 
-            /* Deallocate dinamic memory if it has been used before */
-            delete [] line;
-
             /* Read current line and analyze it*/
-            line = utils::readLine(file);
+            line = utils::readLine(file, buffer);
 
             continue;
         }
@@ -220,19 +192,10 @@ Alignment* clustal_state::LoadAlignment(const std::string &filename)
             i = (i + 1) % alignment->numberOfSequences;
         }
 
-        /* Deallocate dinamic memory if it has been used before */
-        delete [] line;
-
         /* Read current line and analyze it*/
-        line = utils::readLine(file);
+        line = utils::readLine(file, buffer);
     }
 
-    /* Close the input file */
-    file.close();
-
-    /* Deallocate dinamic memory */
-    delete [] line;
-
     /* Check the matrix's content */
     alignment->fillMatrices(true);
     alignment->originalNumberOfSequences = alignment->numberOfSequences;

source/FormatHandling/fasta_m10_state.cpp

@@ -38,7 +38,7 @@ int fasta_m10_state::CheckAlignment(std::istream* origin)
     return 0;
 }
 
-Alignment* fasta_m10_state::LoadAlignment(const std::string &filename)
+Alignment* fasta_m10_state::LoadAlignment(std::istream &file)
 {
     return nullptr;
 }