Add dark theme, logo, and enhance dashboard features - #15
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Apr 6, 2026
* Fixing icode bug * Adding the argument max_gap_helix for merging two close helixes in the pydssp annotation. Also fixing the bug of node_granularity in dashboard (it was missing the parameter in association config dict) * Adding max_gap_helix to the manifest and passing it via config * Add dark theme, logo, and enhance dashboard features (#15) * adding dark theme and also a logo for the program * Increasing the height of mol subviewer * Adding several features to the dashboard. Also adding a temporary logo for the software MHCXGraph. * Distance bug in graph output fixed. Split main.js in small files for management, and implementing a more complete figure exporter * Fixing the hide inactive frames bug * Adding alignment lines while dragging images in editor * Changing the name of modes from `pair` -> `pairwise` and `all` -> `multiple` * Background color fix * Added screening mode * Setting light mode to be the default * Moving hardcode color to CSS variable and updating the color themes to more comfortable colors * Changing the `inc` in `find_value` from `inc = bin_width / 2` to `inc = local_distance_diff_threshold` * Adding `rsa_diff_threshold` and `output_structures` to parameters in manifest * Multiplying the RSA parameters by 100 internally * Fixing the bug that a residue passes in the ASA filter even though it has a RSA value and doesn't pass in RSA filter * Implemented the extension of Graph Color palettes in Dashboard * Optimizing the creation of coherence matrix, reducing the RAM memory usage * Optimization that makes the usage of memory in coherence matrix nearly constant
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