0
Vote

Padena: Use array like access to nodes in DeBruijnGraph to improve GetNodes() method performance

As per the current code a new Stack data structure is created for each call to GetNodes() Method. This method is used in almost all steps of the assembly and in some cases requires more memory than...

Id #7980 | Release: None | Updated: Tue at 10:52 PM by manjus | Created: Tue at 8:58 PM by manjus

0
Vote

Padena: Create Graph step (Including Generate Links) is taking more time.

As per the current implementation DeBruijn nodes are stored in a tree data structure, this tree is not balanced thus takes more time for operations like adding a new node and searching for a partic...

Id #7977 | Release: None | Updated: Mon at 10:34 PM by manjus | Created: Mon at 10:34 PM by manjus

1
Vote

Can't install Bio Ext for Excel because NodeXL installation not recognized

I am trying to install the .Net Bio Extension for Excel 1.01. The Prerequistes dialog says NodelXL is not installed, although I have installed Node Excel Template ver 1.0.201 and can open it in Exc...

Id #7959 | Release: .NET Bio 1.01 | Updated: May 8 at 2:39 PM by sjmercer | Created: May 4 at 5:30 PM by sjmercer

1
Vote

Types in .NET Bio should not implement unnecessary finalizers.

FastASequencePositionParser currently implements a finalizer but has no unmanaged types within the parser itself. This is unnecessary overhead and best practices would push for only using finalize...

Id #7910 | Release: None | Updated: Apr 10 at 6:33 PM by markjulmar | Created: Apr 10 at 6:16 PM by markjulmar

1
Vote

Add mouseover tooltips to assembly and alignment dialogs

The way the current parameters dialogs in BioExcel and the Sequence Assembler are constructed, they display all the parameters needed by an addembler or aligner - and not just the ones that the sel...

Id #7908 | Release: None | Updated: Apr 10 at 3:34 PM by sjmercer | Created: Apr 10 at 3:34 PM by sjmercer

1
Vote

NUCmer algorithm does not directly support reverse matches

NUCmer in Excel does not detect reverse matches, but the commandline NUCmer implementation does so if specified as a commandline switch. This is because the .NET Bio implementation of NUCmer does ...

Id #7889 | Release: None | Updated: Apr 3 at 4:23 PM by sjmercer | Created: Apr 3 at 4:23 PM by sjmercer

0
Vote

Move IMultipleSequenceAligner interface into bio.dll

There is no way currently to identify a multiple-sequence aligner in .NET Bio.  Bio.PamSam includes an IMultipleSequenceAligner interface it uses for this purpose. This interface should be moved to...

Id #7888 | Release: None | Updated: Apr 3 at 4:17 PM by markjulmar | Created: Apr 3 at 4:17 PM by markjulmar

0
Vote

Add option to wrap for Alignment and Concensus views in BioExcel

When we import sequences, we automatically wrap based on a configured column value (80) so you can see the entire sequence data element.  It would be convenient to allow the same sort of display on...

Id #7887 | Release: None | Updated: Apr 3 at 4:14 PM by markjulmar | Created: Apr 3 at 4:14 PM by markjulmar

1
Vote

Sequence Assembler: Scroll bars are very slow

The scroll bars are extremely unresponsive in both the pane displaying all the loaded sequences and in the pane displaying the assembled sequences once an assembly has been done.

Id #7882 | Release: None | Updated: Apr 3 at 4:18 PM by markjulmar | Created: Apr 2 at 10:08 PM by sjmercer

0
Vote

Sequence.Metadata should not be copied across sequences

There are several places where the metadata of a sequence is attached to a second sequence (often generated sequence from an algorithm for example).  The problem is it is a shallow copy of the dict...

Id #7854 | Release: None | Updated: Mar 29 at 3:57 PM by markjulmar | Created: Mar 29 at 3:57 PM by markjulmar