BugFix fasta files marked as decoy where not considered as decoy #141

lutzfischer · 2026-01-27T13:28:13Z

No description provided.

New command line argument --debugfasta

Copilot

Pull request overview

Fixes handling of FASTA files marked as “Decoy” in the GUI and adds explicit CLI support for supplying decoy-only FASTA databases.

Changes:

Add --decoyfasta CLI argument and wire it into sequence loading, disabling auto-decoy generation for that run.
Update GUI process launch args to pass --decoyfasta for FASTA entries flagged as decoy, and add a debug checkbox to optionally start xiSEARCH suspended for JDWP.
Bump version to 1.8.13 and update changelog/version strings.

Reviewed changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 10 comments.

Show a summary per file

File	Description
src/main/java/rappsilber/utils/XiVersion.java	Adds 1.8.13 release notes to embedded change string
src/main/java/rappsilber/gui/SimpleXiGui.java	Passes `--decoyfasta` for decoy-marked FASTAs; adds debug checkbox behavior
src/main/java/rappsilber/gui/SimpleXiGui.form	Adds `ckDebug` component to GUI form layout
src/main/java/rappsilber/config/AbstractRunConfig.java	Adds setter for `autoGenerateDecoys` so CLI can override behavior
src/main/java/rappsilber/applications/Xi.java	Adds parsing/handling for `--decoyfasta` and applies config override
pom.xml	Version/name bump to 1.8.13
Changelog.md	Adds 1.8.13 entry and minor edits

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Copilot · 2026-01-27T13:37:49Z

src/main/java/rappsilber/applications/Xi.java

+        if (decoyFastaArgs.size() >0) {
+            File[] dFastas = new File[decoyFastaArgs.size()];
+            i=0;
+            for (String f : decoyFastaArgs) {
+                dFastas[i++] = new File(f);
+            }
+            SequenceList dSequences = new SequenceList(SequenceList.DECOY_GENERATION.ISDECOY, dFastas, xiconfig);
+            sequences.addAll(dSequences);


sequences.addAll(dSequences) does not update SequenceList's internal m_hasDecoys flag (it’s only updated in addFasta(...)). This makes sequences.hasDecoy() incorrect after adding decoy FASTAs. Consider adding decoy FASTAs via sequences.addFasta(file, ISDECOY) (or otherwise updating the flag) instead of merging via addAll.

Suggested change

if (decoyFastaArgs.size() >0) {

File[] dFastas = new File[decoyFastaArgs.size()];

i=0;

for (String f : decoyFastaArgs) {

dFastas[i++] = new File(f);

}

SequenceList dSequences = new SequenceList(SequenceList.DECOY_GENERATION.ISDECOY, dFastas, xiconfig);

sequences.addAll(dSequences);

if (decoyFastaArgs.size() > 0) {

for (String f : decoyFastaArgs) {

sequences.addFasta(new File(f), SequenceList.DECOY_GENERATION.ISDECOY);

}

Copilot · 2026-01-27T13:37:49Z

src/main/java/rappsilber/utils/XiVersion.java

    public static final String changes = 
+                                "Version 1.8.13\n" +
+                                "  * BugFix: the GUI fasta permited selecting FASTA file as decoy - but that setting was ignored\n" +
+                                "  * new command line argument --decoyfasta adds a FASTA where every proteins is considered decoy - disables autgeneration of decoys\n" +


Grammar issue in changelog entry: "every proteins is" should be singular/plural consistent (e.g., "every protein is" or "all proteins are").

Suggested change

" * new command line argument --decoyfasta adds a FASTA where every proteins is considered decoy - disables autgeneration of decoys\n" +

" * new command line argument --decoyfasta adds a FASTA where every protein is considered decoy - disables autgeneration of decoys\n" +

Copilot · 2026-01-27T13:37:50Z

src/main/java/rappsilber/utils/XiVersion.java


    public static final String changes = 
+                                "Version 1.8.13\n" +
+                                "  * BugFix: the GUI fasta permited selecting FASTA file as decoy - but that setting was ignored\n" +


Typo in changelog entry: "permited" should be "permitted".

Suggested change

" * BugFix: the GUI fasta permited selecting FASTA file as decoy - but that setting was ignored\n" +

" * BugFix: the GUI fasta permitted selecting FASTA file as decoy - but that setting was ignored\n" +

Copilot · 2026-01-27T13:37:50Z

src/main/java/rappsilber/gui/SimpleXiGui.java

+        for (int i = 0 ; i<flFASTAFiles.getFiles().length; i++){ 
+            File f = flFASTAFiles.getFiles()[i];
+            if (flFASTAFiles.isSelected(i)) {
+                args.add("--decoyfasta=" + f.getPath());
+            } else {


flFASTAFiles.getFiles() allocates a new array each call (FileList#getFiles uses toArray). In this loop it's called multiple times per iteration; store the result in a local File[] once before looping to avoid repeated allocations.

Copilot · 2026-01-27T13:37:50Z

src/main/java/rappsilber/gui/SimpleXiGui.java

                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
                .addComponent(ckPeakAnnotations)
-                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 151, Short.MAX_VALUE)


Hard-coding a minimum 151px gap in the GroupLayout (addPreferredGap(..., 151, ...)) can break layout on smaller window sizes and makes the UI less responsive. Prefer DEFAULT_SIZE/0 for the min gap and let the flexible gap (Short.MAX_VALUE) do the spacing.

Suggested change

.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 151, Short.MAX_VALUE)

.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)

Copilot · 2026-01-27T13:37:50Z

Changelog.md

@@ -1,4 +1,8 @@

+Version 1.8.13
+  * BugFix: the GUI fasta permited selecting FASTA file as decoy - but that setting was ignored


Typo in changelog entry: "permited" should be "permitted".

Suggested change

* BugFix: the GUI fasta permited selecting FASTA file as decoy - but that setting was ignored

* BugFix: the GUI fasta permitted selecting FASTA file as decoy - but that setting was ignored

Copilot · 2026-01-27T13:37:51Z

Changelog.md


+Version 1.8.13
+  * BugFix: the GUI fasta permited selecting FASTA file as decoy - but that setting was ignored
+  * new command line argument --decoyfasta adds a FASTA where every proteins is considered decoy - disables autgeneration of decoys


Typo in changelog entry: "autgeneration" should be "auto-generation" (or "autogeneration").

Suggested change

* new command line argument --decoyfasta adds a FASTA where every proteins is considered decoy - disables autgeneration of decoys

* new command line argument --decoyfasta adds a FASTA where every proteins is considered decoy - disables auto-generation of decoys

Copilot · 2026-01-27T13:37:51Z

Changelog.md


 Version 1.8.10
-  * BugFix: on some java versions the actual search did not start
+  * BugFix: under some java versions search faile to start


Typo in changelog entry: "faile" should be "failed".

Suggested change

* BugFix: under some java versions search faile to start

* BugFix: under some java versions search failed to start

Copilot · 2026-01-27T13:37:51Z

Changelog.md


+Version 1.8.13
+  * BugFix: the GUI fasta permited selecting FASTA file as decoy - but that setting was ignored
+  * new command line argument --decoyfasta adds a FASTA where every proteins is considered decoy - disables autgeneration of decoys


Grammar issue in changelog entry: "every proteins is" should be singular/plural consistent (e.g., "every protein is" or "all proteins are").

Suggested change

* new command line argument --decoyfasta adds a FASTA where every proteins is considered decoy - disables autgeneration of decoys

* new command line argument --decoyfasta adds a FASTA where every protein is considered decoy - disables autgeneration of decoys

Copilot · 2026-01-27T13:37:52Z

src/main/java/rappsilber/utils/XiVersion.java

    public static final String changes = 
+                                "Version 1.8.13\n" +
+                                "  * BugFix: the GUI fasta permited selecting FASTA file as decoy - but that setting was ignored\n" +
+                                "  * new command line argument --decoyfasta adds a FASTA where every proteins is considered decoy - disables autgeneration of decoys\n" +


The new change log line has grammar/typo issues (e.g., "every proteins is" / "autgeneration"); please correct to improve clarity (e.g., "every protein is" and "auto-generation").

Suggested change

" * new command line argument --decoyfasta adds a FASTA where every proteins is considered decoy - disables autgeneration of decoys\n" +

" * new command line argument --decoyfasta adds a FASTA where every protein is considered decoy - disables auto-generation of decoys\n" +

Lutz Fischer added 2 commits January 27, 2026 14:06

BugFix fasta files marked as decoy where not considered as decoy

186938a

New command line argument --debugfasta

Updated Changelog

cf94c0d

lutzfischer requested a review from Copilot January 27, 2026 13:28

Copilot started reviewing on behalf of lutzfischer January 27, 2026 13:28 View session

Copilot AI reviewed Jan 27, 2026

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BugFix fasta files marked as decoy where not considered as decoy #141

BugFix fasta files marked as decoy where not considered as decoy #141

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	" * new command line argument --decoyfasta adds a FASTA where every proteins is considered decoy - disables autgeneration of decoys\n" +
	" * new command line argument --decoyfasta adds a FASTA where every protein is considered decoy - disables autgeneration of decoys\n" +

	" * BugFix: the GUI fasta permited selecting FASTA file as decoy - but that setting was ignored\n" +
	" * BugFix: the GUI fasta permitted selecting FASTA file as decoy - but that setting was ignored\n" +

	.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 151, Short.MAX_VALUE)
	.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)

		@@ -1,4 +1,8 @@

		Version 1.8.13
		* BugFix: the GUI fasta permited selecting FASTA file as decoy - but that setting was ignored

	* BugFix: the GUI fasta permited selecting FASTA file as decoy - but that setting was ignored
	* BugFix: the GUI fasta permitted selecting FASTA file as decoy - but that setting was ignored

	* new command line argument --decoyfasta adds a FASTA where every proteins is considered decoy - disables autgeneration of decoys
	* new command line argument --decoyfasta adds a FASTA where every proteins is considered decoy - disables auto-generation of decoys

	* BugFix: under some java versions search faile to start
	* BugFix: under some java versions search failed to start

BugFix fasta files marked as decoy where not considered as decoy #141

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BugFix fasta files marked as decoy where not considered as decoy #141

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lutzfischer commented Jan 27, 2026

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