mirror of
https://github.com/schrodinger/pymol-open-source.git
synced 2026-06-03 19:54:24 +08:00
Add new file streaming API
This commit is contained in:
Cole French
committed by
Thomas Holder
Thomas Holder
parent
2d7d280b79
commit
73fdcdaca6
@@ -13,8 +13,14 @@
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#include <stdlib.h>
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#include "File.h"
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#include "FileStream.h"
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#include "MemoryDebug.h"
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#include <fstream>
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#include <string>
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#include "pymol/zstring_view.h"
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/*
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* Get the size from the current file pointer to the end of the file
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*/
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@@ -84,3 +90,48 @@ char * FileGetContents(const char *filename, long *size) {
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fclose(fp);
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return contents;
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}
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namespace pymol
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{
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#ifdef _WIN32
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std::wstring utf8_to_utf16(pymol::zstring_view utf8)
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{
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std::wstring utf16(utf8.size(), L'\0');
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auto n = MultiByteToWideChar(CP_UTF8, MB_ERR_INVALID_CHARS, utf8.c_str(), -1,
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&utf16[0], utf16.size() + 1);
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if (n == 0) {
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throw std::runtime_error("Could not convert to UTF-16");
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}
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utf16.resize(n - 1);
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return utf16;
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}
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#endif
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static long istream_get_size(std::istream& file)
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{
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auto current = file.tellg();
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file.seekg(0, std::ios::end);
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auto filesize = file.tellg();
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file.seekg(current);
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return filesize;
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}
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static std::string istream_get_contents(std::istream& file)
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{
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auto filesize = istream_get_size(file);
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std::string contents(filesize, '\0');
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file.read(&contents[0], filesize);
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return contents;
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}
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std::string file_get_contents(pymol::zstring_view filename)
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{
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std::ifstream file;
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fstream_open(file, filename, std::ios::in | std::ios::binary);
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return istream_get_contents(file);
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}
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} // namespace pymol
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60
layer0/FileStream.h
Normal file
60
layer0/FileStream.h
Normal file
@@ -0,0 +1,60 @@
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/*
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* Copyright (c) Schrodinger, LLC.
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*
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* Basic file IO with C++ streams.
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*/
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#pragma once
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#include <fstream>
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#include <string>
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#include "pymol/zstring_view.h"
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namespace pymol
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{
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/**
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* Reads entire file into a string
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* @param filename Path in native filesystem encoding or UTF-8
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* @throw ... If file cannot be opened
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*/
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std::string file_get_contents(pymol::zstring_view filename);
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#ifdef _WIN32
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/**
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* Convert UTF-8 to UTF-16
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* @throw ... If input is not valid UTF-8
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*/
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std::wstring utf8_to_utf16(pymol::zstring_view utf8);
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#endif
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/**
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* File stream open wrapper with UTF-8 support on Windows. On Unix, this simply
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* calls `stream.open`.
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*
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* @tparam T std::fstream, std::ifstream, std::ofstream, or a subclass
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* @param stream Stream to open
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* @param filename Path in native filesystem encoding or UTF-8
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* @param mode see std::fstream::open
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* @throw ... If file cannot be opened
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*/
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template <typename T>
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void fstream_open(
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T& stream, zstring_view filename, std::ios_base::openmode mode)
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{
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try {
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stream.open(filename.data(), mode);
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} catch (const std::ios_base::failure&) {
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#ifdef _WIN32
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// On Windows, failure may be due to filename being UTF-8
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auto wfilename = utf8_to_utf16(filename);
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// Windows overloads open to support a wchar_t array
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stream.open(wfilename.c_str(), mode);
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#else
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throw;
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#endif
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}
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}
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} // namespace pymol
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// vi:ft=cpp:sw=2
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@@ -27,7 +27,7 @@ Z* -------------------------------------------------------------------
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#include"Util.h"
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#include"Feedback.h"
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#include"Parse.h"
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#include"File.h"
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#include"FileStream.h"
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#ifndef int2
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typedef int int2[2];
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@@ -225,39 +225,40 @@ int MatchPreScore(CMatch * I, int *vla1, int n1, int *vla2, int n2, int quiet)
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#define BLOSUM62_ROWS 33
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#define BLOSUM62_COLS 80
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static char blosum62[BLOSUM62_ROWS][BLOSUM62_COLS] = {
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static const char blosum62[] = {
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#if 0
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"# Matrix made by matblas from blosum62.iij\n",
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"# * column uses minimum score\n",
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"# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units\n",
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"# Blocks Database = /data/blocks_5.0/blocks.dat\n",
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"# Cluster Percentage: >= 62\n",
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"# Entropy = 0.6979, Expected = -0.5209\n",
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" A R N D C Q E G H I L K M F P S T W Y V B Z X *\n",
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"A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4\n",
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"R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -4\n",
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"N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4\n",
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"D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4\n",
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"C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4\n",
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"Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4\n",
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"E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4\n",
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"G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4\n",
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"H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4\n",
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"I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 -3 -1 -4\n",
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"L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 -3 -1 -4\n",
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"K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4\n",
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"M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -4\n",
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"F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4\n",
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"P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -4\n",
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"S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4\n",
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"T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 0 -4\n",
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"W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -3 -2 -4\n",
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"Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -4\n",
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"V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4\n",
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"B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -4\n",
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"Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4\n",
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"X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4\n",
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"* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1\n",
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""
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#endif
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" A R N D C Q E G H I L K M F P S T W Y V B Z X *\n"
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"A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4\n"
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"R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -4\n"
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"N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4\n"
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"D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4\n"
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"C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4\n"
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"Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4\n"
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"E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4\n"
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"G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4\n"
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"H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4\n"
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"I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 -3 -1 -4\n"
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"L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 -3 -1 -4\n"
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"K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4\n"
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"M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -4\n"
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"F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4\n"
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"P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -4\n"
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"S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4\n"
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"T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 0 -4\n"
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"W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -3 -2 -4\n"
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"Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -4\n"
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"V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4\n"
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"B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -4\n"
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"Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4\n"
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"X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4\n"
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"* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1\n"
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};
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int MatchMatrixFromFile(CMatch * I, const char *fname, int quiet)
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@@ -265,8 +266,8 @@ int MatchMatrixFromFile(CMatch * I, const char *fname, int quiet)
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PyMOLGlobals *G = I->G;
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int ok = 1;
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char *buffer = NULL;
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char *p;
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std::string buffer;
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const char *p;
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char cc[255];
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char *code = NULL;
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unsigned int x, y;
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@@ -279,32 +280,22 @@ int MatchMatrixFromFile(CMatch * I, const char *fname, int quiet)
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&& !(strcmp(fname, "BLOSUM62") == 0)
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#endif
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) {
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buffer = FileGetContents(fname, NULL);
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if (!buffer) {
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try {
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buffer = pymol::file_get_contents(fname);
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} catch (...) {
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PRINTFB(G, FB_Match, FB_Errors)
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" Match-Error: unable to open matrix file '%s'.\n", fname ENDFB(G);
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ok = false;
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}
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} else {
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buffer = pymol::malloc<char>(BLOSUM62_ROWS * BLOSUM62_COLS);
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if(buffer) {
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p = buffer;
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a = 0;
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while(blosum62[a][0]) {
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strcpy(p, &blosum62[a][0]);
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p += strlen(p);
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a++;
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}
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} else {
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ok = false;
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}
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buffer = blosum62;
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}
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if(ok && buffer) {
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if(ok && !buffer.empty()) {
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/* count codes */
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p = buffer;
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p = buffer.c_str();
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n_entry = 0;
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while(*p && ok) {
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switch (*p) {
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@@ -325,7 +316,7 @@ int MatchMatrixFromFile(CMatch * I, const char *fname, int quiet)
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/* read codes */
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p = buffer;
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p = buffer.c_str();
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n_entry = 0;
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while(*p && ok) {
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switch (*p) {
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@@ -343,7 +334,7 @@ int MatchMatrixFromFile(CMatch * I, const char *fname, int quiet)
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/* read values */
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p = buffer;
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p = buffer.c_str();
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while((*p) && ok) {
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switch (*p) {
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case '#':
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@@ -364,7 +355,6 @@ int MatchMatrixFromFile(CMatch * I, const char *fname, int quiet)
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p = ParseNextLine(p);
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}
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}
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mfree(buffer);
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}
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if(ok) {
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if(!quiet) {
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@@ -31,7 +31,7 @@ Z* -------------------------------------------------------------------
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#include "Util.h"
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#include "Util2.h"
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#include "Texture.h"
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#include "File.h"
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#include "FileStream.h"
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#include "Matrix.h"
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#include "Parse.h"
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@@ -438,7 +438,7 @@ string CShaderMgr::GetShaderSource(const string &filename)
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return it->second;
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}
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char* buffer = nullptr;
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std::string buffer;
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const char *pl = nullptr, *newpl, *tpl;
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std::ostringstream newbuffer;
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@@ -457,9 +457,10 @@ string CShaderMgr::GetShaderSource(const string &filename)
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string path(pymol_data);
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path.append(PATH_SEP).append("shaders").append(PATH_SEP).append(filename);
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pl = buffer = FileGetContents(path.c_str(), nullptr);
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if (!buffer) {
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try {
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buffer = pymol::file_get_contents(path);
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pl = buffer.c_str();
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} catch (...) {
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PRINTFB(G, FB_ShaderMgr, FB_Warnings)
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" Warning: shaders_from_dist=on, but unable to open file '%s'\n",
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path.c_str() ENDFB(G);
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@@ -547,8 +548,6 @@ string CShaderMgr::GetShaderSource(const string &filename)
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}
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}
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FreeP(buffer);
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string result = newbuffer.str();
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shader_cache_processed[filename] = result;
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return result;
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