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from-FoldSeek workflow. various UI/UX improvements #115

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980f054
from-FoldSeek workflow. various UI/UX improvements
dannydoor Sep 30, 2025
65ac0cb
Build static server binaries
milot-mirdita Sep 17, 2025
47ff429
Add a -version switch to print git commit
milot-mirdita Sep 17, 2025
e73e5e7
allow overriding parameters like the GPU parameters in the cli
milot-mirdita Sep 18, 2025
3660bd5
1. Editted code style
dannydoor Oct 14, 2025
1802bf4
Merge branch 'master' into fromSeek
dannydoor Oct 14, 2025
ac2007a
Fixed prepending comment to support mmCIF format
dannydoor Oct 15, 2025
09e4768
Fixed issue with fetching structure files from pdb100 db
dannydoor Oct 15, 2025
372e225
Fixed select-all help icon be hidden when select-all button is checked
dannydoor Oct 15, 2025
8c2b5b0
Fixed Foldseek Multimer-to-FoldMason workflow: concatenate multiple c…
dannydoor Oct 17, 2025
11256d1
Added floating navigation button
dannydoor Oct 21, 2025
9527bf7
Navigation button now works properly
dannydoor Oct 22, 2025
afaccf3
Fixed NavigationButton file name
dannydoor Oct 22, 2025
b12bba4
Fixed select-to-send buttons style to be compatible with navigation b…
dannydoor Oct 22, 2025
cb1fe1c
Fixed file name, removed unnecessary logs
dannydoor Oct 22, 2025
8917b7f
Fixed the rest of the path in ResultFoldMason.vue
dannydoor Oct 22, 2025
62d613f
1. Fixed pulchra-related alignment structure loading bug.
dannydoor Nov 5, 2025
a7ee2b7
Refactored codes for optimization and easier maintenance.
dannydoor Nov 7, 2025
71a5baa
Fixed table mode switch button.
dannydoor Nov 7, 2025
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74 changes: 71 additions & 3 deletions frontend/FoldMasonSearch.vue
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@
@click:close="removeQuery(index)"
>
{{ q.name }}
</v-chip>
</v-chip>
</div>
</div>

Expand Down Expand Up @@ -131,6 +131,9 @@ import { HistoryMixin } from './lib/HistoryMixin.js';
import Databases from './Databases.vue';
import QueryTextarea from "./QueryTextarea.vue";
import DragUploadBox from "./DragUploadBox.vue";
import { BlobDatabase } from "./lib/BlobDatabase.js";

const db = BlobDatabase();

export default {
name: "FoldMasonSearch",
Expand Down Expand Up @@ -160,8 +163,9 @@ export default {
async mounted() {
if (this.preloadAccessions.length > 0) {
this.queries = [];
return;
}
this.retrieveAndClean()
return;
},
computed: {
alignDisabled() {
Expand Down Expand Up @@ -253,7 +257,7 @@ export default {
async removeQuery(index) {
this.queries.splice(index, 1);
},
async addFiles(newFiles) {
addFiles(newFiles) {
for (const newFile of newFiles) {
if (!this.fileNameSet.has(newFile.name)) {
this.queries.push(newFile);
Expand Down Expand Up @@ -297,6 +301,70 @@ export default {
);
fr.readAsText(file)
},
resetParams() {
this.params = structuredClone(defaultParams);
},
async retrieveAndClean() {
const clean = async (size) => {
// return
await db.removeItem('msa.query.size')
await db.removeItem('msa.query.names')
for (let i = 0; i < size; i++) {
await db.removeItem(`msa.query.chunk:${i}`)
}
}

// await clean(2)
// return

const SEP = '\0'

let size = await db.getItem('msa.query.size')
if (!size || size.length == 0) {
await clean()
return
}

size = parseInt(size)

const texts = []
let names = await db.getItem('msa.query.names')
if (!names || names.length == 0) {
console.warn("MSA query name has not been passed")
await clean(size)
return
}
names = names.split(SEP)

for (let i = 0; i < size; i++) {
const entry = await db.getItem(`msa.query.chunk:${i}`)
if (!entry || entry.length == 0) {
console.warn(`MSA query chunk ${i} is missing`)
await clean(size)
return
}

texts.push(...( ( await entry.text() ).split(SEP) ))
}

if (names.length != texts.length) {
console.warn("MSA query entries and names size differs")
console.log(`names length: ${names.length}`)
console.log(`texts length: ${texts.length}`)
await clean(size)
return
}

const files = []

for (let i = 0; i < texts.length; i++) {
files.push({text: texts[i], name: names[i]})
}

this.addFiles(files)

await clean(size)
}
}
};
</script>
Expand Down
192 changes: 102 additions & 90 deletions frontend/MDI.js
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,96 +1,108 @@
import {
mdiAlertCircleOutline as AlertCircleOutline,
mdiArrowRightCircle as ArrowRightCircle,
mdiArrowRightCircleOutline as ArrowRightCircleOutline,
mdiAxisZRotateCounterclockwise as AxisZRotateCounterclockwise,
mdiChevronLeft as ChevronLeft,
mdiChevronRight as ChevronRight,
mdiCircle as Circle,
mdiCircleHalf as CircleHalf,
mdiClockOutline as ClockOutline,
mdiCloudDownloadOutline as CloudDownloadOutline,
mdiDelete as Delete,
mdiDns as Dns,
mdiFile as File,
mdiFileUpload as FileUpload,
mdiFileDownloadOutline as FileDownloadOutline,
mdiFormatListBulleted as FormatListBulleted,
mdiFullscreen as Fullscreen,
mdiHelpCircleOutline as HelpCircleOutline,
mdiHistory as History,
mdiLabel as Label,
mdiLabelOutline as LabelOutline,
mdiMagnify as Magnify,
mdiMinusBox as MinusBox,
mdiNotificationClearAll as NotificationClearAll,
mdiPlusBox as PlusBox,
mdiProgressWrench as ProgressWrench,
mdiReorderHorizontal as ReorderHorizontal,
mdiRestore as Restore,
mdiTableLarge as TableLarge,
mdiTune as Tune,
mdiLayersSearchOutline as LayersSearchOutline,
mdiCloseCircle as CloseCircle,
mdiCloseCircleOutline as CloseCircleOutline,
mdiWall as Wall,
mdiTextBoxOutline as TextBoxOutline,
mdiPencil as Pencil,
} from '@mdi/js';
mdiAlertCircleOutline as AlertCircleOutline,
mdiArrowRightCircle as ArrowRightCircle,
mdiArrowRightCircleOutline as ArrowRightCircleOutline,
mdiAxisZRotateCounterclockwise as AxisZRotateCounterclockwise,
mdiChevronLeft as ChevronLeft,
mdiChevronRight as ChevronRight,
mdiChevronUp as ChevronUp,
mdiChevronDown as ChevronDown,
mdiCircle as Circle,
mdiCircleHalf as CircleHalf,
mdiClockOutline as ClockOutline,
mdiCloudDownloadOutline as CloudDownloadOutline,
mdiDelete as Delete,
mdiDns as Dns,
mdiFile as File,
mdiFileUpload as FileUpload,
mdiFileDownloadOutline as FileDownloadOutline,
mdiFormatListBulleted as FormatListBulleted,
mdiFullscreen as Fullscreen,
mdiHelpCircleOutline as HelpCircleOutline,
mdiHistory as History,
mdiLabel as Label,
mdiLabelOutline as LabelOutline,
mdiMagnify as Magnify,
mdiMinusBox as MinusBox,
mdiNotificationClearAll as NotificationClearAll,
mdiPlusBox as PlusBox,
mdiProgressWrench as ProgressWrench,
mdiReorderHorizontal as ReorderHorizontal,
mdiRestore as Restore,
mdiTableLarge as TableLarge,
mdiTune as Tune,
mdiLayersSearchOutline as LayersSearchOutline,
mdiCloseCircle as CloseCircle,
mdiCloseCircleOutline as CloseCircleOutline,
mdiWall as Wall,
mdiTextBoxOutline as TextBoxOutline,
mdiPencil as Pencil,
mdiChevronDoubleUp as DoubleChevronUp,
} from "@mdi/js";

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"M 22.23 1.96 c -0.98 0 -1.77 0.8 -1.77 1.77 c 0 0.21 0.05 0.4 0.12 0.6 l -8.31 14.23 c -0.8 0.17 -1.42 0.85 -1.42 1.7 a 1.77 1.77 0 0 0 3.54 0 c 0 -0.2 -0.05 -0.37 -0.1 -0.55 l 8.34 -14.29 a 1.75 1.75 0 0 0 1.37 -1.69 c 0 -0.97 -0.8 -1.77 -1.77 -1.77 M 14.98 1.96 c -0.98 0 -1.77 0.8 -1.77 1.77 c 0 0.21 0.05 0.4 0.12 0.6 l -8.3 14.24 c -0.81 0.16 -1.43 0.84 -1.43 1.7 a 1.77 1.77 0 0 0 3.55 0 c 0 -0.2 -0.06 -0.38 -0.12 -0.56 L 15.4 5.42 a 1.75 1.75 0 0 0 1.37 -1.69 c 0 -0.97 -0.8 -1.77 -1.78 -1.77 M 1.75 6 a 1.75 1.75 0 1 0 0 3.5 a 1.75 1.75 0 0 0 0 -3.5 z m 0 6 a 1.75 1.75 0 1 0 0 3.5 a 1.75 1.75 0 0 0 0 -3.5 z";
const Monomer =
"m13.9 4.4.8.5a7.7 7.7 90 0 0 1.3.6 2.3 2.3 90 0 1 .5.2l.5.2.4.2.1.2a.4.4 90 0 1-.1.3A6.2 6.2 90 0 1 16 7a11.3 11.3 0 0 0-1.2.6l-.5-.2-1.1-.6a2 2 0 0 1-.5-.6 1.8 1.8 90 0 1-.2-1V3A5.3 5.3 90 0 0 14 4.4Zm-1.6-2c-.4-.8-1-1.3-1.6-1.3-1-.1-1.7.3-2.2 1.2a4.2 4.2 90 0 0-.3 1.3H10v12.9h2l-3.4 3.4.1 1.6c0 .4-.1.5-.4.5-.2 0 1.2-1-.4-.4L7.6 20l-3.3-3.4h1.9V3.6h1.1a7.4 7.4 90 0 1 .5-1.7C8.3.7 9.3.1 10.8.2a2.2 2.2 90 0 1 1.2.6A4.3 4.3 90 0 1 13 2v.3c0 .2 0 .4-.3.4-.2 0-.3 0-.4-.2Zm4.3 20.8a3 3 0 0 1-2.6-.5c-.8-.5-1.2-1.4-1.2-2.7 0-.3.1-.4.4-.4.3 0 .4.1.4.4 0 1 .3 1.7.8 2a2.5 2.5 90 0 0 2 .3h.1c.3 0 .5.2.5.5 0 .2-.1.3-.4.4Zm1.4-8v1a2.1 2.1 90 0 1-.3.5 2.6 2.6 90 0 1-.8.5l-.7.3-.6.3c-1.3.4-2 .7-2 .8a2.5 2.5 90 0 0-.8.5l-.2.3a3.3 3.3 90 0 1-.1-.8 5 5 90 0 1 0-1.3 2.4 2.4 90 0 1 .4-.8 3.6 3.6 90 0 1 .6-.4 38.4 38.4 0 0 1 4-1.9l.2-.3a2.6 2.6 90 0 1 .2.3 3.2 3.2 90 0 1 0 1Zm-5.2-1.8V13l.2-.4.7-.5 1-.3a7.7 7.7 90 0 0 1.3.6l.5.2.5.2.4.2.1.2-.1.2a2.4 2.4 90 0 1-.8.4 3 3 90 0 0-.5.2 1.9 1.9 90 0 1-.6.2l-.7.4-.5-.3a4.6 4.6 90 0 1-1.1-.5l-.2-.3-.2-.2ZM18 8.2a5.8 5.8 90 0 1 0 1 1.2 1.2 90 0 1-.3.5l-.5.3a189.3 189.3 90 0 0-3.6 1.5 2.5 2.5 90 0 0-.8.6l-.2.3-.1-.7v-1.3l.4-.9.5-.3L15.6 8l.6-.3a3.5 3.5 90 0 1 .5-.2l.9-.4.2-.3v.2l.2 1.1Z";
const Multimer =
"M14 19.3c0-.3.2-.4.3-.5h.2c.3 0 .4.1.4.3.1.8.4 1.4 1 1.7.5.2 1 .3 1.5.1H17.7c.2-.1.4 0 .5.2 0 .3 0 .4-.3.5l-.4.2h-.3c-.5.1-1 0-1.7-.3-.4-.1-.7-.4-.9-.8a2.4 2.4 0 0 1-.4-1l-.1-.4Zm3.2-2h-.4a18.4 18.4 0 0 0-2.6.8l-.2.3v-.7c0-.5.1-.8.3-1l.6-.7.5-.3A63.2 63.2 0 0 1 18 15l.5-.2h.3l.3-.1.1-.1.3-.3v.2a7.5 7.5 0 0 1-.2 1.9l-.2.4-.8.4a15 15 0 0 0-.8.1h-.2Zm-5.1-.1v.6h-.6l-.4-.5-.6-.7-4.6-.8 1.5-1-5.9-8 .9-.7-.6-1.5c-.3-1.3.2-2.4 1.3-3.1l1.3-.3h.4l.4.1.2.1.6.4c.2 0 .3.2.2.5l-.4.2h-.2l-.4-.2-.8-.2c-.3 0-.6 0-.9.2a2 2 0 0 0-1 2.2l.6 1.1 1.3-1 1 1.4L5 8.6l1.4-1 3.8 5 1.5-1-.6 4.6.9 1Zm7-4-.1.3-.8.3a9 9 0 0 0-1.7.4 100.6 100.6 0 0 1-1.4-1.1v-.5c0-.1 0-.3.2-.4l.7-.3.8-.2.1.1.5.3.6.3a2092.6 2092.6 0 0 0 1.1.8Zm-8-2L7.2 6l-1.1.8.6-4 4 .7-1.1.8 4.2 5.7c-.4.5-.5 1.5-.4 3l-.6.4-.7-.9.2-2.2-1.2 1Zm9.2-3.7v1.2l-.2.8c0 .3-.2.4-.2.4l-.5.3a49.2 49.2 0 0 1-4.1 1l-.2.3V11c0-.4 0-.8.2-1.1l.5-.7.4-.3a19.2 19.2 0 0 1 4-1V7.4Zm-3.9-4.2c.3.5.6.9 1 1.1.2.4.5.6.6.6l.5.3a15.8 15.8 0 0 1 .8.6h.3l.1.2h.2c0 .2.2.3.3.3V7h-.5a2 2 0 0 0-.3.2l-.5.1-.5.1h-.1l-.3.1a1 1 0 0 0-.3 0l-.5-.2a4.7 4.7 0 0 1-1-1l-.2-.2V5l.4-2v.3Zm1.9-1.8c.1 0 .9-1.4 0-1.1-.9.2-1.5.7-1.8 1.5 0 .4 0 .7.5.8.4 0 .6-.1.7-.5 0-.3.3-.5.6-.7Z";
const Motif =
"m12.42 17.45.15 1.38a.8.8 0 0 0 .34.57l1.69 1.4a.8.8 0 0 0 1.02-1.23l-1.5-1.24-.14-1.3 1.79-2.67-2.53-3.22-3.84 1.4.16 4.1 2.86.81Zm.4-1.55-1.71-.48-.07-1.77 1.66-.61 1.1 1.39-.99 1.47Zm-.3-6.77a2.4 2.4 0 1 0-3.02 1.52h-.01a2.4 2.4 0 0 0 3.02-1.52Zm7.03-3.1-2.21-2.32-3.7 1.77.55 4.05 4.02.74 1.42-2.62L21 7.8a.8.8 0 0 0 .62-.2l1.74-1.34a.8.8 0 0 0-.98-1.27l-1.54 1.19-1.3-.14Zm-1.35.9-.84 1.56-1.74-.32-.24-1.75 1.6-.77 1.22 1.28ZM4.57.05.69.55A.8.8 0 0 0 .9 2.16l3.58-.48L6.96 5a.8.8 0 0 0 1.28-.95L5.61.5a.8.8 0 0 0-.54-.46.8.8 0 0 0-.5 0Z";

export default {
AlertCircleOutline,
ApplicationBracesOutline,
ArrowRightCircle,
ArrowRightCircleOutline,
AxisZRotateCounterclockwise,
ChevronLeft,
ChevronRight,
Circle,
CircleHalf,
CircleOneThird,
CircleTwoThird,
ClockOutline,
CloudDownloadOutline,
Delete,
Dns,
File,
FileDownloadOutline,
FileUpload,
FormatListBulleted,
Fullscreen,
HelpCircleOutline,
History,
Label,
LabelOutline,
Magnify,
MinusBox,
NotificationClearAll,
PlusBox,
ProgressWrench,
ReorderHorizontal,
Restore,
SavePDB,
SavePNG,
TableLarge,
Tune,
LayersSearchOutline,
API,
CloseCircle,
CloseCircleOutline,
Monomer,
Multimer,
Wall,
TextBoxOutline,
Motif,
Pencil,
};
AlertCircleOutline,
ApplicationBracesOutline,
ArrowRightCircle,
ArrowRightCircleOutline,
AxisZRotateCounterclockwise,
ChevronLeft,
ChevronRight,
ChevronUp,
ChevronDown,
Circle,
CircleHalf,
CircleOneThird,
CircleTwoThird,
ClockOutline,
CloudDownloadOutline,
Delete,
Dns,
File,
FileDownloadOutline,
FileUpload,
FormatListBulleted,
Fullscreen,
HelpCircleOutline,
History,
Label,
LabelOutline,
Magnify,
MinusBox,
NotificationClearAll,
PlusBox,
ProgressWrench,
ReorderHorizontal,
Restore,
SavePDB,
SavePNG,
TableLarge,
Tune,
LayersSearchOutline,
API,
CloseCircle,
CloseCircleOutline,
Monomer,
Multimer,
Wall,
TextBoxOutline,
Motif,
Pencil,
DoubleChevronUp,
};
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