adds fragment frequencies to fragments overview by JonasSchaub · Pull Request #213 · FelixBaensch/MORTAR

JonasSchaub · 2026-01-16T17:42:56Z

closes #186

This PR adds fragment frequency labels to the fragment overview view and a general screenshot functionality to the overview view. Also included are several code quality improvements behind the scenes

Copilot

Pull request overview

This PR adds the display of fragment frequencies in the fragments overview view. When viewing fragments from the fragments tab, each fragment image now shows its frequency count and percentage below the molecular structure.

Changes:

Refactored repeated Graphics2D rendering configuration into a reusable configureGraphics2D method
Added a new depictImageWithTextForOverview method that supports both transparent and white backgrounds for images with text labels
Introduced frequency display logic to show fragment counts and percentages in the overview view for fragments tab data

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 5 comments.

File	Description
DepictionUtil.java	Refactored rendering hints configuration and added new method to depict images with text labels supporting configurable backgrounds
OverviewViewController.java	Added frequency display flag and logic to show fragment frequencies in the overview view

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src/main/java/de/unijena/cheminf/mortar/model/depict/DepictionUtil.java

src/main/java/de/unijena/cheminf/mortar/controller/OverviewViewController.java

sonarqubecloud · 2026-01-16T19:04:50Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

JonasSchaub · 2026-01-16T19:37:26Z

Example picture:

…o depict image with text methods

…ncies) from being wider than the image

Copilot

Pull request overview

Copilot reviewed 8 out of 8 changed files in this pull request and generated 10 comments.

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src/main/java/de/unijena/cheminf/mortar/model/depict/DepictionUtil.java

src/main/java/de/unijena/cheminf/mortar/controller/OverviewViewController.java

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

…s test class for DepictionUtil

Copilot

Pull request overview

Copilot reviewed 10 out of 10 changed files in this pull request and generated 5 comments.

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src/main/java/de/unijena/cheminf/mortar/model/depict/DepictionUtil.java

src/test/java/de/unijena/cheminf/mortar/model/depict/DepictionUtilTest.java

Copilot

Pull request overview

Copilot reviewed 13 out of 13 changed files in this pull request and generated 3 comments.

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src/main/java/de/unijena/cheminf/mortar/model/depict/DepictionUtil.java

src/main/java/de/unijena/cheminf/mortar/controller/OverviewViewController.java

Copilot

Pull request overview

Copilot reviewed 15 out of 15 changed files in this pull request and generated 3 comments.

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src/main/java/de/unijena/cheminf/mortar/model/util/FileUtil.java

src/main/java/de/unijena/cheminf/mortar/controller/OverviewViewController.java

src/main/java/de/unijena/cheminf/mortar/model/depict/DepictionUtil.java

Copilot

Pull request overview

Copilot reviewed 15 out of 15 changed files in this pull request and generated 2 comments.

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src/main/java/de/unijena/cheminf/mortar/controller/OverviewViewController.java

…k into separate method

Copilot

Pull request overview

Copilot reviewed 15 out of 15 changed files in this pull request and generated 5 comments.

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src/main/java/de/unijena/cheminf/mortar/controller/OverviewViewController.java

src/main/java/de/unijena/cheminf/mortar/model/util/FileUtil.java

src/main/java/de/unijena/cheminf/mortar/gui/views/ItemizationDataTableView.java

Copilot

Pull request overview

Copilot reviewed 15 out of 15 changed files in this pull request and generated 2 comments.

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src/main/java/de/unijena/cheminf/mortar/controller/OverviewViewController.java

src/main/java/de/unijena/cheminf/mortar/model/depict/DepictionUtil.java

sonarqubecloud · 2026-04-08T21:54:07Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

Copilot

Pull request overview

Copilot reviewed 15 out of 15 changed files in this pull request and generated no new comments.

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JonasSchaub · 2026-04-08T22:35:12Z

To do: final (human) code review

JonasSchaub · 2026-04-08T22:35:22Z

To do: update tutorial

JonasSchaub self-assigned this Jan 16, 2026

JonasSchaub added the enhancement New feature or request label Jan 16, 2026

JonasSchaub added 2 commits January 16, 2026 19:45

adds fragment frequencies to fragments overview

9b952fc

encapsulates Graphics2D config to reduce duplication

84167e0

JonasSchaub force-pushed the issue-186-fragment-freqs-overview branch from 3ffb0ce to 84167e0 Compare January 16, 2026 18:45

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code formatting and comments according to Copilot review

a2b05c7

JonasSchaub added 5 commits April 1, 2026 14:28

Merge branch 'production' into issue-186-fragment-freqs-overview

808a718

unifies distances in image with text depiction and unifies the the tw…

db576df

…o depict image with text methods

adds checks and routines to prevent text labels in depictions (freque…

89b7732

…ncies) from being wider than the image

refactoring

bd47ec3

adds screenshot functionality and button to the overview view

e5b37e1

JonasSchaub marked this pull request as ready for review April 1, 2026 16:23

JonasSchaub requested a review from Copilot April 1, 2026 16:24

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JonasSchaub and others added 7 commits April 2, 2026 11:53

makes FORMATS array thread-safe

5164055

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

dispose Graphics2D instance after method call

a47dd90

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

use BufferedImage.TYPE_INT_RGB instead of Transparency.OPAQUE

bec01dd

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

revert usage of ThreadLocal again, the clean-up would be too complicated

fd79b19

removes decimal formats that make no sense for integer values and add…

bec7618

…s test class for DepictionUtil

implements remaining Copilot suggestions

22a514d

use constants for standard font

5d7b17f

JonasSchaub requested a review from Copilot April 2, 2026 12:38

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actually assign the sanitized file name to the variable and correct doc

99726eb

JonasSchaub requested a review from Copilot April 8, 2026 12:38

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JonasSchaub added 3 commits April 8, 2026 18:15

gives speaking names to DepictionUtil methods

95fa667

fixes spotless complaint

4355973

fixes Copilot complaints

a266768

JonasSchaub requested a review from Copilot April 8, 2026 16:38

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fixes Copilot complaints

0dfe467

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src/main/java/de/unijena/cheminf/mortar/controller/OverviewViewController.java Show resolved Hide resolved

src/main/java/de/unijena/cheminf/mortar/controller/OverviewViewController.java Outdated Show resolved Hide resolved

make file extension check locale-sensitive and extract screenshot tas…

81aef13

…k into separate method

JonasSchaub requested a review from Copilot April 8, 2026 17:49

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JonasSchaub added 2 commits April 8, 2026 20:07

implements Copilot suggestions

e6e8353

reuses font metrics for every cell render in items tab

9035b22

JonasSchaub requested a review from Copilot April 8, 2026 18:20

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src/main/java/de/unijena/cheminf/mortar/controller/OverviewViewController.java Outdated Show resolved Hide resolved

src/main/java/de/unijena/cheminf/mortar/model/depict/DepictionUtil.java Show resolved Hide resolved

implements Copilot suggestions

3a7761c

JonasSchaub requested a review from Copilot April 8, 2026 21:53

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sonarqubecloud bot commented Apr 8, 2026

Quality Gate passed

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JonasSchaub commented Jan 16, 2026 •

edited

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