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• Is there a Boost (or other common lib) type for matrices with string keys?

  - by mohawkjohn

  I have a dense matrix where the indices correspond to genes. While gene identifiers are often integers, they are not contiguous integers. They could be strings instead, too. I suppose I could use a boost sparse matrix of some sort with integer keys, and it wouldn't matter if they're contiguous. Or would this still occupy a great deal of space, particularly if some genes have identifiers that are nine digits? Further, I am concerned that sparse storage is not appropriate, since this is an all-by-all matrix (there will be a distance in each and every cell, provided the gene exists). I'm unlikely to need to perform any matrix operations (e.g., matrix multiplication). I will need to pull vectors out of the matrix (slices). It seems like the best type of matrix would be keyed by a Boost unordered_map (a hash map), or perhaps even simply an STL map. Am I looking at this the wrong way? Do I really need to roll my own? I thought I saw such a class somewhere before. Thanks!

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• How would I instruct extconf.rb to use additional g++ optimization flags, and which are advisable?

  - by mohawkjohn

  I'm using Rice to write a C++ extension for a Ruby gem. The extension is in the form of a shared object (.so) file. This requires 'mkmf-rice' instead of 'mkmf', but the two (AFAIK) are pretty similar. By default, the compiler uses the flags -g -O2. Personally, I find this kind of silly, since it's hard to debug with any optimization enabled. I've resorted to editing the Makefile to take out the flags I don't like (e.g., removing -fPIC -shared when I need to debug using main() instead of Ruby's hooks). But I figure there's got to be a better way. I know I can just do $CPPFLAGS += " -DRICE" to add additional flags. But how do I remove things without editing the Makefile directly? A secondary question: what optimizations are safe for shared objects loaded by Ruby? Can I do things like -funroll-loops? What do you all recommend? It's a scientific computing project, so the faster the better. Memory is not much of an issue. Many thanks!

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• How does one write extconf.rb files when one extension includes header files from another?

  - by mohawkjohn

  This is a follow-up question for: Multiple Ruby modules under one directory What happens if these extensions include each other? For example, you have the following structure: ext/foo ext/bar In ext/bar/bar.h, you have a #include "foo.h" foo.h and foo.cpp compile to form foo.o, to make life a little more complicated. Finally, it is necessary that foo and bar be separate extensions. How is this managed? I can't figure out how to add ../foo to the search path for bar.h, primarily. Symbolic links seem hack-ish.

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• Can you recommend an in-browser Ruby/Rails 3D renderer?

  - by mohawkjohn

  I want to draw some 3D network diagrams in a web browser, and the data for these diagrams are in a Rails app (in the database). I already use flotomatic as a Rails interface for pretty Javascript plots (e.g., independent variable, dependent variable). Certainly there are packages for drawing simple things in Javascript. What I'm looking for is (a) a Javascript package for 3D drawings that are displayed in a web browser (without a plugin), and (b) a Ruby API for that package, if possible. Any recommendations? Many thanks!

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