egps-TQTools (SeqTools)

This repository is an extension module collection for eGPS2, focused on biological sequence analysis tools and workflow panels (SeqTools).

• 中文说明请看：README_zh.md

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Project Positioning

• This project is a collection of eGPS2 desktop modules (Swing). The source code lives under src/, and the dependency JARs live under dependency-egps/.
• The repository currently exposes 28 public module entry points, counted by modules that implement IModuleLoader and excluding internal subpanels.
• The table below lists every module entry point, its source location, and a short description.

Module Overview

#	Module Name	Entry Class	Description
1	Analyse homogeneous with species tree	src/module/analysehomogene/IndependentModuleLoader.java	Infers homologous genes from species-tree information using the parsimony principle.
2	Back mutation presenter	src/module/backmutpres/IndependentModuleLoader.java	Text visualization of back mutations.
3	Batch Peptides Operator	src/module/batchpepo/IndependentModuleLoader.java	A pipeline for batch-processing multiple peptide sequences.
4	Bed merger	src/module/bedmerger/IndependentModuleLoader.java	Merges BED files according to record coordinates.
5	Batch Ensembl annotation downloader	src/module/benchensdownloader/IndependentModuleLoader.java	Bulk-downloads Ensembl annotation files such as CDS, protein, and GFF3.
6	Direct sequence mapping	src/module/brutemapping/IndependentModuleLoader.java	Maps short sequences to the genome using the Knuth-Morris-Pratt algorithm.
7	Correlation visualization for WNT	src/module/correlation4wnt/ModuleLoader.java	Correlation visualization for the Wnt pathway.
8	Datetime calculator	src/module/datetimecalculator/IndependentModuleLoader.java	Quickly generates date/time values from string entries.
9	Fasta dumper	src/module/fastadumper/IndependentModuleLoader.java	Quickly exports FASTA content, with support for gap removal, renaming, and substring extraction.
10	Fasta Tools	src/module/fastatools/IndependentModuleLoader.java	A collection of FASTA file processing tools.
11	GEO Supplementary File Processor	src/module/geoprocessor/IndependentModuleLoader.java	Convenient processing of GEO supplementary files.
12	GFF3 operator	src/module/gff3opr/IndependentModuleLoader.java	Quickly extracts information from GFF-formatted files.
13	Quick histogram	src/module/histogram/IndependentModuleLoader.java	Quickly draws histograms from data series.
14	Homologous gene identification	src/module/homoidentify/IndependentModuleLoader.java	Identifies homologous genes with BLAST and HMMER.
15	Line break eliminator	src/module/linebEliminator/IndependentModuleLoader.java	Quickly removes redundant line breaks from a paragraph.
16	Local blast wrapper	src/module/localblast/gui/IndependentModuleLoader.java	A wrapper for running local BLAST and processing the results.
17	MA plot	src/module/maplot/IndependentModuleLoader.java	A convenient tool for drawing MA plots.
18	Multi-seqs struct view	src/module/multiseqview/IndependentModuleLoader.java	A structure-visualization tool for multiple sequences, including domains and motifs.
19	Extract text by regex	src/module/regexExtract/IndependentModuleLoader.java	Extracts target text using regular expressions.
20	Sequence logo	src/module/sequencelogo/IndependentModuleLoader.java	A convenient tool for drawing sequence logos.
21	Skeleton scatter plot	src/module/skeletonscatter/IndependentModuleLoader.java	A basic skeleton scatter plot for demonstrating visualization and computation capabilities.
22	String set operator	src/module/stringsetoperator/IndependentModuleLoader.java	Convenient operations on string sets.
23	Table-like text curation	src/module/tablecuration/IndependentModuleLoader.java	Multiple tools for curating table-like text files.
24	Table-like text view	src/module/tablelikeview/IndependentModuleLoader.java	Quickly view table-like data imported from TSV/CSV files.
25	Theoretical target genes with motif	src/module/targetoftf/IndependentModuleLoader.java	Infers theoretical target genes from binding motifs on the genome.
26	Two strings comparator	src/module/twostringcomp/IndependentModuleLoader.java	Compares two strings, which is useful for checking pairwise alignment results.
27	Bio. sequence operator	src/operator/sequences/IndependentModuleLoader.java	A collection of line-by-line operations for single sequences.
28	Primary Struct Drawer	src/primary/struct/display/IndependentModuleLoader.java	Draws protein structures with domain annotations.

Requirements

• JDK: 25
• JDK 25 on this machine:
  • /home/dell/software/java25/jdk-25+36/bin/javac
  • /home/dell/software/java25/jdk-25+36/bin/java

Build (manual)

/home/dell/software/java25/jdk-25+36/bin/javac \
  -d ./out/production/egps-TQTools \
  -cp "dependency-egps/*" \
  $(find src -name "*.java")

To reproduce/check compile warnings (recommended when cleaning warnings):

/home/dell/software/java25/jdk-25+36/bin/javac -Xlint:all -Xmaxwarns 10000 \
  -d ./out/production/egps-TQTools \
  -cp "dependency-egps/*" \
  $(find src -name "*.java")

See remove_compile_warnings.md for the warning-cleanup notes.

Package as JAR (optional)

jar -cf egps-TQTools.jar -C ./out/production/egps-TQTools .

Deploy into eGPS2 (concept)

Typically, you copy the compiled output (or egps-TQTools.jar) into eGPS2's dependency-egps/, then let eGPS2 load it via its module/plugin system.

Note: this repo contains module code only; it does not include the eGPS2 main entry (egps2.Launcher). You need the eGPS2 main project to run the application.

Runtime args (JDK module access)

eGPS.args includes a set of --add-exports/--add-opens flags to keep some UI dependencies (e.g., JIDE) working on newer JDKs.

• When launching the eGPS2 main application, you typically pass it as @eGPS.args, e.g. /home/dell/software/java25/jdk-25+36/bin/java ... @eGPS.args ...
• The eGPS.args in this repo is a reference; follow your eGPS2 main project/distribution requirements if they differ