@rtemis/a3 0.1.0

package/LICENSE.txt

@@ -0,0 +1,373 @@
+Mozilla Public License Version 2.0
+==================================
+
+1. Definitions
+--------------
+
+1.1. "Contributor"
+    means each individual or legal entity that creates, contributes to
+    the creation of, or owns Covered Software.
+
+1.2. "Contributor Version"
+    means the combination of the Contributions of others (if any) used
+    by a Contributor and that particular Contributor's Contribution.
+
+1.3. "Contribution"
+    means Covered Software of a particular Contributor.
+
+1.4. "Covered Software"
+    means Source Code Form to which the initial Contributor has attached
+    the notice in Exhibit A, the Executable Form of such Source Code
+    Form, and Modifications of such Source Code Form, in each case
+    including portions thereof.
+
+1.5. "Incompatible With Secondary Licenses"
+    means
+
+    (a) that the initial Contributor has attached the notice described
+        in Exhibit B to the Covered Software; or
+
+    (b) that the Covered Software was made available under the terms of
+        version 1.1 or earlier of the License, but not also under the
+        terms of a Secondary License.
+
+1.6. "Executable Form"
+    means any form of the work other than Source Code Form.
+
+1.7. "Larger Work"
+    means a work that combines Covered Software with other material, in 
+    a separate file or files, that is not Covered Software.
+
+1.8. "License"
+    means this document.
+
+1.9. "Licensable"
+    means having the right to grant, to the maximum extent possible,
+    whether at the time of the initial grant or subsequently, any and
+    all of the rights conveyed by this License.
+
+1.10. "Modifications"
+    means any of the following:
+
+    (a) any file in Source Code Form that results from an addition to,
+        deletion from, or modification of the contents of Covered
+        Software; or
+
+    (b) any new file in Source Code Form that contains any Covered
+        Software.
+
+1.11. "Patent Claims" of a Contributor
+    means any patent claim(s), including without limitation, method,
+    process, and apparatus claims, in any patent Licensable by such
+    Contributor that would be infringed, but for the grant of the
+    License, by the making, using, selling, offering for sale, having
+    made, import, or transfer of either its Contributions or its
+    Contributor Version.
+
+1.12. "Secondary License"
+    means either the GNU General Public License, Version 2.0, the GNU
+    Lesser General Public License, Version 2.1, the GNU Affero General
+    Public License, Version 3.0, or any later versions of those
+    licenses.
+
+1.13. "Source Code Form"
+    means the form of the work preferred for making modifications.
+
+1.14. "You" (or "Your")
+    means an individual or a legal entity exercising rights under this
+    License. For legal entities, "You" includes any entity that
+    controls, is controlled by, or is under common control with You. For
+    purposes of this definition, "control" means (a) the power, direct
+    or indirect, to cause the direction or management of such entity,
+    whether by contract or otherwise, or (b) ownership of more than
+    fifty percent (50%) of the outstanding shares or beneficial
+    ownership of such entity.
+
+2. License Grants and Conditions
+--------------------------------
+
+2.1. Grants
+
+Each Contributor hereby grants You a world-wide, royalty-free,
+non-exclusive license:
+
+(a) under intellectual property rights (other than patent or trademark)
+    Licensable by such Contributor to use, reproduce, make available,
+    modify, display, perform, distribute, and otherwise exploit its
+    Contributions, either on an unmodified basis, with Modifications, or
+    as part of a Larger Work; and
+
+(b) under Patent Claims of such Contributor to make, use, sell, offer
+    for sale, have made, import, and otherwise transfer either its
+    Contributions or its Contributor Version.
+
+2.2. Effective Date
+
+The licenses granted in Section 2.1 with respect to any Contribution
+become effective for each Contribution on the date the Contributor first
+distributes such Contribution.
+
+2.3. Limitations on Grant Scope
+
+The licenses granted in this Section 2 are the only rights granted under
+this License. No additional rights or licenses will be implied from the
+distribution or licensing of Covered Software under this License.
+Notwithstanding Section 2.1(b) above, no patent license is granted by a
+Contributor:
+
+(a) for any code that a Contributor has removed from Covered Software;
+    or
+
+(b) for infringements caused by: (i) Your and any other third party's
+    modifications of Covered Software, or (ii) the combination of its
+    Contributions with other software (except as part of its Contributor
+    Version); or
+
+(c) under Patent Claims infringed by Covered Software in the absence of
+    its Contributions.
+
+This License does not grant any rights in the trademarks, service marks,
+or logos of any Contributor (except as may be necessary to comply with
+the notice requirements in Section 3.4).
+
+2.4. Subsequent Licenses
+
+No Contributor makes additional grants as a result of Your choice to
+distribute the Covered Software under a subsequent version of this
+License (see Section 10.2) or under the terms of a Secondary License (if
+permitted under the terms of Section 3.3).
+
+2.5. Representation
+
+Each Contributor represents that the Contributor believes its
+Contributions are its original creation(s) or it has sufficient rights
+to grant the rights to its Contributions conveyed by this License.
+
+2.6. Fair Use
+
+This License is not intended to limit any rights You have under
+applicable copyright doctrines of fair use, fair dealing, or other
+equivalents.
+
+2.7. Conditions
+
+Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted
+in Section 2.1.
+
+3. Responsibilities
+-------------------
+
+3.1. Distribution of Source Form
+
+All distribution of Covered Software in Source Code Form, including any
+Modifications that You create or to which You contribute, must be under
+the terms of this License. You must inform recipients that the Source
+Code Form of the Covered Software is governed by the terms of this
+License, and how they can obtain a copy of this License. You may not
+attempt to alter or restrict the recipients' rights in the Source Code
+Form.
+
+3.2. Distribution of Executable Form
+
+If You distribute Covered Software in Executable Form then:
+
+(a) such Covered Software must also be made available in Source Code
+    Form, as described in Section 3.1, and You must inform recipients of
+    the Executable Form how they can obtain a copy of such Source Code
+    Form by reasonable means in a timely manner, at a charge no more
+    than the cost of distribution to the recipient; and
+
+(b) You may distribute such Executable Form under the terms of this
+    License, or sublicense it under different terms, provided that the
+    license for the Executable Form does not attempt to limit or alter
+    the recipients' rights in the Source Code Form under this License.
+
+3.3. Distribution of a Larger Work
+
+You may create and distribute a Larger Work under terms of Your choice,
+provided that You also comply with the requirements of this License for
+the Covered Software. If the Larger Work is a combination of Covered
+Software with a work governed by one or more Secondary Licenses, and the
+Covered Software is not Incompatible With Secondary Licenses, this
+License permits You to additionally distribute such Covered Software
+under the terms of such Secondary License(s), so that the recipient of
+the Larger Work may, at their option, further distribute the Covered
+Software under the terms of either this License or such Secondary
+License(s).
+
+3.4. Notices
+
+You may not remove or alter the substance of any license notices
+(including copyright notices, patent notices, disclaimers of warranty,
+or limitations of liability) contained within the Source Code Form of
+the Covered Software, except that You may alter any license notices to
+the extent required to remedy known factual inaccuracies.
+
+3.5. Application of Additional Terms
+
+You may choose to offer, and to charge a fee for, warranty, support,
+indemnity or liability obligations to one or more recipients of Covered
+Software. However, You may do so only on Your own behalf, and not on
+behalf of any Contributor. You must make it absolutely clear that any
+such warranty, support, indemnity, or liability obligation is offered by
+You alone, and You hereby agree to indemnify every Contributor for any
+liability incurred by such Contributor as a result of warranty, support,
+indemnity or liability terms You offer. You may include additional
+disclaimers of warranty and limitations of liability specific to any
+jurisdiction.
+
+4. Inability to Comply Due to Statute or Regulation
+---------------------------------------------------
+
+If it is impossible for You to comply with any of the terms of this
+License with respect to some or all of the Covered Software due to
+statute, judicial order, or regulation then You must: (a) comply with
+the terms of this License to the maximum extent possible; and (b)
+describe the limitations and the code they affect. Such description must
+be placed in a text file included with all distributions of the Covered
+Software under this License. Except to the extent prohibited by statute
+or regulation, such description must be sufficiently detailed for a
+recipient of ordinary skill to be able to understand it.
+
+5. Termination
+--------------
+
+5.1. The rights granted under this License will terminate automatically
+if You fail to comply with any of its terms. However, if You become
+compliant, then the rights granted under this License from a particular
+Contributor are reinstated (a) provisionally, unless and until such
+Contributor explicitly and finally terminates Your grants, and (b) on an
+ongoing basis, if such Contributor fails to notify You of the
+non-compliance by some reasonable means prior to 60 days after You have
+come back into compliance. Moreover, Your grants from a particular
+Contributor are reinstated on an ongoing basis if such Contributor
+notifies You of the non-compliance by some reasonable means, this is the
+first time You have received notice of non-compliance with this License
+from such Contributor, and You become compliant prior to 30 days after
+Your receipt of the notice.
+
+5.2. If You initiate litigation against any entity by asserting a patent
+infringement claim (excluding declaratory judgment actions,
+counter-claims, and cross-claims) alleging that a Contributor Version
+directly or indirectly infringes any patent, then the rights granted to
+You by any and all Contributors for the Covered Software under Section
+2.1 of this License shall terminate.
+
+5.3. In the event of termination under Sections 5.1 or 5.2 above, all
+end user license agreements (excluding distributors and resellers) which
+have been validly granted by You or Your distributors under this License
+prior to termination shall survive termination.
+
+************************************************************************
+*                                                                      *
+*  6. Disclaimer of Warranty                                           *
+*  -------------------------                                           *
+*                                                                      *
+*  Covered Software is provided under this License on an "as is"       *
+*  basis, without warranty of any kind, either expressed, implied, or  *
+*  statutory, including, without limitation, warranties that the       *
+*  Covered Software is free of defects, merchantable, fit for a        *
+*  particular purpose or non-infringing. The entire risk as to the     *
+*  quality and performance of the Covered Software is with You.        *
+*  Should any Covered Software prove defective in any respect, You     *
+*  (not any Contributor) assume the cost of any necessary servicing,   *
+*  repair, or correction. This disclaimer of warranty constitutes an   *
+*  essential part of this License. No use of any Covered Software is   *
+*  authorized under this License except under this disclaimer.         *
+*                                                                      *
+************************************************************************
+
+************************************************************************
+*                                                                      *
+*  7. Limitation of Liability                                          *
+*  --------------------------                                          *
+*                                                                      *
+*  Under no circumstances and under no legal theory, whether tort      *
+*  (including negligence), contract, or otherwise, shall any           *
+*  Contributor, or anyone who distributes Covered Software as          *
+*  permitted above, be liable to You for any direct, indirect,         *
+*  special, incidental, or consequential damages of any character      *
+*  including, without limitation, damages for lost profits, loss of    *
+*  goodwill, work stoppage, computer failure or malfunction, or any    *
+*  and all other commercial damages or losses, even if such party      *
+*  shall have been informed of the possibility of such damages. This   *
+*  limitation of liability shall not apply to liability for death or   *
+*  personal injury resulting from such party's negligence to the       *
+*  extent applicable law prohibits such limitation. Some               *
+*  jurisdictions do not allow the exclusion or limitation of           *
+*  incidental or consequential damages, so this exclusion and          *
+*  limitation may not apply to You.                                    *
+*                                                                      *
+************************************************************************
+
+8. Litigation
+-------------
+
+Any litigation relating to this License may be brought only in the
+courts of a jurisdiction where the defendant maintains its principal
+place of business and such litigation shall be governed by laws of that
+jurisdiction, without reference to its conflict-of-law provisions.
+Nothing in this Section shall prevent a party's ability to bring
+cross-claims or counter-claims.
+
+9. Miscellaneous
+----------------
+
+This License represents the complete agreement concerning the subject
+matter hereof. If any provision of this License is held to be
+unenforceable, such provision shall be reformed only to the extent
+necessary to make it enforceable. Any law or regulation which provides
+that the language of a contract shall be construed against the drafter
+shall not be used to construe this License against a Contributor.
+
+10. Versions of the License
+---------------------------
+
+10.1. New Versions
+
+Mozilla Foundation is the license steward. Except as provided in Section
+10.3, no one other than the license steward has the right to modify or
+publish new versions of this License. Each version will be given a
+distinguishing version number.
+
+10.2. Effect of New Versions
+
+You may distribute the Covered Software under the terms of the version
+of the License under which You originally received the Covered Software,
+or under the terms of any subsequent version published by the license
+steward.
+
+10.3. Modified Versions
+
+If you create software not governed by this License, and you want to
+create a new license for such software, you may create and use a
+modified version of this License if you rename the license and remove
+any references to the name of the license steward (except to note that
+such modified license differs from this License).
+
+10.4. Distributing Source Code Form that is Incompatible With Secondary
+Licenses
+
+If You choose to distribute Source Code Form that is Incompatible With
+Secondary Licenses under the terms of this version of the License, the
+notice described in Exhibit B of this License must be attached.
+
+Exhibit A - Source Code Form License Notice
+-------------------------------------------
+
+  This Source Code Form is subject to the terms of the Mozilla Public
+  License, v. 2.0. If a copy of the MPL was not distributed with this
+  file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+If it is not possible or desirable to put the notice in a particular
+file, then You may include the notice in a location (such as a LICENSE
+file in a relevant directory) where a recipient would be likely to look
+for such a notice.
+
+You may add additional accurate notices of copyright ownership.
+
+Exhibit B - "Incompatible With Secondary Licenses" Notice
+---------------------------------------------------------
+
+  This Source Code Form is "Incompatible With Secondary Licenses", as
+  defined by the Mozilla Public License, v. 2.0.

package/dist/a3.d.ts

@@ -0,0 +1,43 @@
+import type { ZodError } from "zod";
+import { type A3Data, type VariantData } from "./schemas";
+export declare class A3ValidationError extends Error {
+    readonly issues: ZodError["issues"];
+    constructor(zodError: ZodError);
+}
+export declare class A3ParseError extends Error {
+    constructor(message: string, options?: ErrorOptions);
+}
+export declare class A3 {
+    #private;
+    constructor(input: unknown);
+    static fromData(data: unknown): A3;
+    static fromJSONText(text: string): A3;
+    /** Number of residues in the sequence. */
+    get length(): number;
+    /**
+     * Return the residue at a 1-based position.
+     * Throws RangeError if position is out of bounds.
+     */
+    residueAt(position: number): string;
+    /**
+     * Return all variants at a given 1-based position.
+     */
+    variantsAt(position: number): VariantData[];
+    /**
+     * Return the canonical validated data object.
+     * The returned reference is frozen — spread to get a mutable copy.
+     */
+    toData(): A3Data;
+    /**
+     * Return the canonical data object for JSON serialization.
+     * Called automatically by JSON.stringify — do not return a string here.
+     */
+    toJSON(): A3Data;
+    /**
+     * Serialize to a JSON string.
+     * @param indent Number of spaces for indentation (default 2). Pass 0 for compact output.
+     */
+    toJSONString(indent?: number): string;
+    toString(): string;
+}
+//# sourceMappingURL=a3.d.ts.map

package/dist/a3.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"a3.d.ts","sourceRoot":"","sources":["../src/a3.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,KAAK,CAAC;AACpC,OAAO,EAAE,KAAK,MAAM,EAAiB,KAAK,WAAW,EAAE,MAAM,WAAW,CAAC;AAIzE,qBAAa,iBAAkB,SAAQ,KAAK;IAC1C,QAAQ,CAAC,MAAM,EAAE,QAAQ,CAAC,QAAQ,CAAC,CAAC;gBAExB,QAAQ,EAAE,QAAQ;CAK/B;AAED,qBAAa,YAAa,SAAQ,KAAK;gBACzB,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,YAAY;CAIpD;AAID,qBAAa,EAAE;;gBAGD,KAAK,EAAE,OAAO;IAQ1B,MAAM,CAAC,QAAQ,CAAC,IAAI,EAAE,OAAO,GAAG,EAAE;IAIlC,MAAM,CAAC,YAAY,CAAC,IAAI,EAAE,MAAM,GAAG,EAAE;IAcrC,0CAA0C;IAC1C,IAAI,MAAM,IAAI,MAAM,CAEnB;IAED;;;OAGG;IACH,SAAS,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM;IASnC;;OAEG;IACH,UAAU,CAAC,QAAQ,EAAE,MAAM,GAAG,WAAW,EAAE;IAM3C;;;OAGG;IACH,MAAM,IAAI,MAAM;IAIhB;;;OAGG;IACH,MAAM,IAAI,MAAM;IAIhB;;;OAGG;IACH,YAAY,CAAC,MAAM,SAAI,GAAG,MAAM;IAMhC,QAAQ,IAAI,MAAM;CAOnB"}

package/dist/a3.js

@@ -0,0 +1,93 @@
+import { A3InputSchema } from "./schemas";
+// ── Error classes ─────────────────────────────────────────────────────────────
+export class A3ValidationError extends Error {
+    issues;
+    constructor(zodError) {
+        super(zodError.message);
+        this.name = "A3ValidationError";
+        this.issues = zodError.issues;
+    }
+}
+export class A3ParseError extends Error {
+    constructor(message, options) {
+        super(message, options);
+        this.name = "A3ParseError";
+    }
+}
+// ── A3 class ──────────────────────────────────────────────────────────────────
+export class A3 {
+    #data;
+    constructor(input) {
+        const result = A3InputSchema.safeParse(input);
+        if (!result.success)
+            throw new A3ValidationError(result.error);
+        this.#data = Object.freeze(result.data);
+    }
+    // ── Static constructors ───────────────────────────────────────────────────
+    static fromData(data) {
+        return new A3(data);
+    }
+    static fromJSONText(text) {
+        let parsed;
+        try {
+            parsed = JSON.parse(text);
+        }
+        catch (e) {
+            throw new A3ParseError("Invalid JSON", { cause: e });
+        }
+        return new A3(parsed);
+    }
+    // readJSON is provided in io.ts and re-exported from index.ts
+    // ── Accessors ─────────────────────────────────────────────────────────────
+    /** Number of residues in the sequence. */
+    get length() {
+        return this.#data.sequence.length;
+    }
+    /**
+     * Return the residue at a 1-based position.
+     * Throws RangeError if position is out of bounds.
+     */
+    residueAt(position) {
+        if (!Number.isInteger(position) || position < 1 || position > this.length) {
+            throw new RangeError(`position ${position} is out of bounds for sequence of length ${this.length} (must be 1–${this.length})`);
+        }
+        return this.#data.sequence.charAt(position - 1);
+    }
+    /**
+     * Return all variants at a given 1-based position.
+     */
+    variantsAt(position) {
+        return this.#data.annotations.variant.filter((v) => v.position === position);
+    }
+    // ── Serialization ─────────────────────────────────────────────────────────
+    /**
+     * Return the canonical validated data object.
+     * The returned reference is frozen — spread to get a mutable copy.
+     */
+    toData() {
+        return this.#data;
+    }
+    /**
+     * Return the canonical data object for JSON serialization.
+     * Called automatically by JSON.stringify — do not return a string here.
+     */
+    toJSON() {
+        return this.#data;
+    }
+    /**
+     * Serialize to a JSON string.
+     * @param indent Number of spaces for indentation (default 2). Pass 0 for compact output.
+     */
+    toJSONString(indent = 2) {
+        return JSON.stringify(this, null, indent);
+    }
+    // ── Introspection ─────────────────────────────────────────────────────────
+    toString() {
+        const seq = this.#data.sequence;
+        const preview = seq.length > 12 ? `${seq.slice(0, 12)}…` : seq;
+        const id = this.#data.metadata.uniprot_id;
+        const label = id ? ` [${id}]` : "";
+        return `A3${label} { length: ${this.length}, sequence: "${preview}" }`;
+    }
+}
+//# sourceMappingURL=a3.js.map

package/dist/a3.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"a3.js","sourceRoot":"","sources":["../src/a3.ts"],"names":[],"mappings":"AACA,OAAO,EAAe,aAAa,EAAoB,MAAM,WAAW,CAAC;AAEzE,iFAAiF;AAEjF,MAAM,OAAO,iBAAkB,SAAQ,KAAK;IACjC,MAAM,CAAqB;IAEpC,YAAY,QAAkB;QAC5B,KAAK,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC;QACxB,IAAI,CAAC,IAAI,GAAG,mBAAmB,CAAC;QAChC,IAAI,CAAC,MAAM,GAAG,QAAQ,CAAC,MAAM,CAAC;IAChC,CAAC;CACF;AAED,MAAM,OAAO,YAAa,SAAQ,KAAK;IACrC,YAAY,OAAe,EAAE,OAAsB;QACjD,KAAK,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;QACxB,IAAI,CAAC,IAAI,GAAG,cAAc,CAAC;IAC7B,CAAC;CACF;AAED,iFAAiF;AAEjF,MAAM,OAAO,EAAE;IACJ,KAAK,CAAS;IAEvB,YAAY,KAAc;QACxB,MAAM,MAAM,GAAG,aAAa,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC;QAC9C,IAAI,CAAC,MAAM,CAAC,OAAO;YAAE,MAAM,IAAI,iBAAiB,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;QAC/D,IAAI,CAAC,KAAK,GAAG,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;IAC1C,CAAC;IAED,6EAA6E;IAE7E,MAAM,CAAC,QAAQ,CAAC,IAAa;QAC3B,OAAO,IAAI,EAAE,CAAC,IAAI,CAAC,CAAC;IACtB,CAAC;IAED,MAAM,CAAC,YAAY,CAAC,IAAY;QAC9B,IAAI,MAAe,CAAC;QACpB,IAAI,CAAC;YACH,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;QAC5B,CAAC;QAAC,OAAO,CAAC,EAAE,CAAC;YACX,MAAM,IAAI,YAAY,CAAC,cAAc,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC,CAAC;QACvD,CAAC;QACD,OAAO,IAAI,EAAE,CAAC,MAAM,CAAC,CAAC;IACxB,CAAC;IAED,8DAA8D;IAE9D,6EAA6E;IAE7E,0CAA0C;IAC1C,IAAI,MAAM;QACR,OAAO,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,MAAM,CAAC;IACpC,CAAC;IAED;;;OAGG;IACH,SAAS,CAAC,QAAgB;QACxB,IAAI,CAAC,MAAM,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,QAAQ,GAAG,CAAC,IAAI,QAAQ,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC;YAC1E,MAAM,IAAI,UAAU,CAClB,YAAY,QAAQ,4CAA4C,IAAI,CAAC,MAAM,eAAe,IAAI,CAAC,MAAM,GAAG,CACzG,CAAC;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,MAAM,CAAC,QAAQ,GAAG,CAAC,CAAC,CAAC;IAClD,CAAC;IAED;;OAEG;IACH,UAAU,CAAC,QAAgB;QACzB,OAAO,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,KAAK,QAAQ,CAAC,CAAC;IAC/E,CAAC;IAED,6EAA6E;IAE7E;;;OAGG;IACH,MAAM;QACJ,OAAO,IAAI,CAAC,KAAK,CAAC;IACpB,CAAC;IAED;;;OAGG;IACH,MAAM;QACJ,OAAO,IAAI,CAAC,KAAK,CAAC;IACpB,CAAC;IAED;;;OAGG;IACH,YAAY,CAAC,MAAM,GAAG,CAAC;QACrB,OAAO,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,EAAE,MAAM,CAAC,CAAC;IAC5C,CAAC;IAED,6EAA6E;IAE7E,QAAQ;QACN,MAAM,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC;QAChC,MAAM,OAAO,GAAG,GAAG,CAAC,MAAM,GAAG,EAAE,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC;QAC/D,MAAM,EAAE,GAAG,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,UAAU,CAAC;QAC1C,MAAM,KAAK,GAAG,EAAE,CAAC,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;QACnC,OAAO,KAAK,KAAK,cAAc,IAAI,CAAC,MAAM,gBAAgB,OAAO,KAAK,CAAC;IACzE,CAAC;CACF"}

package/dist/index.d.ts

@@ -0,0 +1,4 @@
+export { A3, A3ValidationError, A3ParseError } from "./a3";
+export { readJSON, writeJSON } from "./io";
+export type { A3Data, MetadataData, VariantData, SiteEntryData, RegionEntryData, FlexEntryData, } from "./schemas";
+//# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,EAAE,EAAE,iBAAiB,EAAE,YAAY,EAAE,MAAM,MAAM,CAAC;AAC3D,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAE,MAAM,MAAM,CAAC;AAC3C,YAAY,EACV,MAAM,EACN,YAAY,EACZ,WAAW,EACX,aAAa,EACb,eAAe,EACf,aAAa,GACd,MAAM,WAAW,CAAC"}

package/dist/index.js

@@ -0,0 +1,3 @@
+export { A3, A3ValidationError, A3ParseError } from "./a3";
+export { readJSON, writeJSON } from "./io";
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,EAAE,EAAE,iBAAiB,EAAE,YAAY,EAAE,MAAM,MAAM,CAAC;AAC3D,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAE,MAAM,MAAM,CAAC"}

package/dist/io.d.ts

@@ -0,0 +1,14 @@
+import { A3 } from "./a3";
+/**
+ * Read an A3 JSON file from disk and return a validated A3 instance.
+ * @param path Absolute or relative path to a .json file.
+ */
+export declare function readJSON(path: string): Promise<A3>;
+/**
+ * Write an A3 instance to a JSON file.
+ * @param a3    The A3 instance to serialize.
+ * @param path  Absolute or relative path to write.
+ * @param indent Number of spaces for indentation (default 2).
+ */
+export declare function writeJSON(a3: A3, path: string, indent?: number): Promise<void>;
+//# sourceMappingURL=io.d.ts.map

package/dist/io.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"io.d.ts","sourceRoot":"","sources":["../src/io.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,EAAE,EAAgB,MAAM,MAAM,CAAC;AAExC;;;GAGG;AACH,wBAAsB,QAAQ,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,EAAE,CAAC,CAQxD;AAED;;;;;GAKG;AACH,wBAAsB,SAAS,CAAC,EAAE,EAAE,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE,MAAM,SAAI,GAAG,OAAO,CAAC,IAAI,CAAC,CAO/E"}

package/dist/io.js

@@ -0,0 +1,32 @@
+import { readFile, writeFile } from "node:fs/promises";
+import { A3, A3ParseError } from "./a3";
+/**
+ * Read an A3 JSON file from disk and return a validated A3 instance.
+ * @param path Absolute or relative path to a .json file.
+ */
+export async function readJSON(path) {
+    let text;
+    try {
+        text = await readFile(path, "utf-8");
+    }
+    catch (e) {
+        throw new A3ParseError(`Cannot read file: ${path}`, { cause: e });
+    }
+    return A3.fromJSONText(text);
+}
+/**
+ * Write an A3 instance to a JSON file.
+ * @param a3    The A3 instance to serialize.
+ * @param path  Absolute or relative path to write.
+ * @param indent Number of spaces for indentation (default 2).
+ */
+export async function writeJSON(a3, path, indent = 2) {
+    const text = a3.toJSONString(indent);
+    try {
+        await writeFile(path, text, "utf-8");
+    }
+    catch (e) {
+        throw new A3ParseError(`Cannot write file: ${path}`, { cause: e });
+    }
+}
+//# sourceMappingURL=io.js.map

package/dist/io.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"io.js","sourceRoot":"","sources":["../src/io.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAC;AACvD,OAAO,EAAE,EAAE,EAAE,YAAY,EAAE,MAAM,MAAM,CAAC;AAExC;;;GAGG;AACH,MAAM,CAAC,KAAK,UAAU,QAAQ,CAAC,IAAY;IACzC,IAAI,IAAY,CAAC;IACjB,IAAI,CAAC;QACH,IAAI,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC;IACvC,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,MAAM,IAAI,YAAY,CAAC,qBAAqB,IAAI,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC,CAAC;IACpE,CAAC;IACD,OAAO,EAAE,CAAC,YAAY,CAAC,IAAI,CAAC,CAAC;AAC/B,CAAC;AAED;;;;;GAKG;AACH,MAAM,CAAC,KAAK,UAAU,SAAS,CAAC,EAAM,EAAE,IAAY,EAAE,MAAM,GAAG,CAAC;IAC9D,MAAM,IAAI,GAAG,EAAE,CAAC,YAAY,CAAC,MAAM,CAAC,CAAC;IACrC,IAAI,CAAC;QACH,MAAM,SAAS,CAAC,IAAI,EAAE,IAAI,EAAE,OAAO,CAAC,CAAC;IACvC,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,MAAM,IAAI,YAAY,CAAC,sBAAsB,IAAI,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC,CAAC;IACrE,CAAC;AACH,CAAC"}

package/dist/normalize.d.ts

@@ -0,0 +1,17 @@
+/**
+ * Sort and deduplicate a position array.
+ * Input positions are assumed valid (positive integers) — validated by Zod before calling.
+ */
+export declare function sortDedup(arr: readonly number[]): number[];
+/**
+ * Sort ranges by start position (then end position for ties).
+ * Input ranges are assumed valid (start < end) — validated by Zod before calling.
+ * Overlap detection is handled separately in the schema layer.
+ */
+export declare function sortRanges(arr: readonly [number, number][]): [number, number][];
+/**
+ * Recursively check that a value is JSON-compatible.
+ * Rejects undefined, functions, symbols, and class instances.
+ */
+export declare function isJsonCompatible(v: unknown): boolean;
+//# sourceMappingURL=normalize.d.ts.map

package/dist/normalize.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"normalize.d.ts","sourceRoot":"","sources":["../src/normalize.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,wBAAgB,SAAS,CAAC,GAAG,EAAE,SAAS,MAAM,EAAE,GAAG,MAAM,EAAE,CAE1D;AAED;;;;GAIG;AACH,wBAAgB,UAAU,CAAC,GAAG,EAAE,SAAS,CAAC,MAAM,EAAE,MAAM,CAAC,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,EAAE,CAE/E;AAED;;;GAGG;AACH,wBAAgB,gBAAgB,CAAC,CAAC,EAAE,OAAO,GAAG,OAAO,CAUpD"}

package/dist/normalize.js

@@ -0,0 +1,35 @@
+/**
+ * Sort and deduplicate a position array.
+ * Input positions are assumed valid (positive integers) — validated by Zod before calling.
+ */
+export function sortDedup(arr) {
+    return [...new Set(arr)].sort((a, b) => a - b);
+}
+/**
+ * Sort ranges by start position (then end position for ties).
+ * Input ranges are assumed valid (start < end) — validated by Zod before calling.
+ * Overlap detection is handled separately in the schema layer.
+ */
+export function sortRanges(arr) {
+    return [...arr].sort((a, b) => a[0] - b[0] || a[1] - b[1]);
+}
+/**
+ * Recursively check that a value is JSON-compatible.
+ * Rejects undefined, functions, symbols, and class instances.
+ */
+export function isJsonCompatible(v) {
+    if (v === null)
+        return true;
+    if (typeof v === "boolean" || typeof v === "number" || typeof v === "string")
+        return true;
+    if (Array.isArray(v))
+        return v.every(isJsonCompatible);
+    if (typeof v === "object") {
+        const proto = Object.getPrototypeOf(v);
+        if (proto !== Object.prototype && proto !== null)
+            return false;
+        return Object.values(v).every(isJsonCompatible);
+    }
+    return false;
+}
+//# sourceMappingURL=normalize.js.map

package/dist/normalize.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"normalize.js","sourceRoot":"","sources":["../src/normalize.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,MAAM,UAAU,SAAS,CAAC,GAAsB;IAC9C,OAAO,CAAC,GAAG,IAAI,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;AACjD,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,UAAU,CAAC,GAAgC;IACzD,OAAO,CAAC,GAAG,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;AAC7D,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,gBAAgB,CAAC,CAAU;IACzC,IAAI,CAAC,KAAK,IAAI;QAAE,OAAO,IAAI,CAAC;IAC5B,IAAI,OAAO,CAAC,KAAK,SAAS,IAAI,OAAO,CAAC,KAAK,QAAQ,IAAI,OAAO,CAAC,KAAK,QAAQ;QAAE,OAAO,IAAI,CAAC;IAC1F,IAAI,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QAAE,OAAO,CAAC,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC;IACvD,IAAI,OAAO,CAAC,KAAK,QAAQ,EAAE,CAAC;QAC1B,MAAM,KAAK,GAAG,MAAM,CAAC,cAAc,CAAC,CAAC,CAAY,CAAC;QAClD,IAAI,KAAK,KAAK,MAAM,CAAC,SAAS,IAAI,KAAK,KAAK,IAAI;YAAE,OAAO,KAAK,CAAC;QAC/D,OAAO,MAAM,CAAC,MAAM,CAAC,CAA4B,CAAC,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC;IAC7E,CAAC;IACD,OAAO,KAAK,CAAC;AACf,CAAC"}

package/dist/schemas.d.ts

@@ -0,0 +1,294 @@
+import { z } from "zod";
+declare const SiteEntrySchema: z.ZodObject<{
+    index: z.ZodEffects<z.ZodArray<z.ZodNumber, "many">, number[], number[]>;
+    type: z.ZodDefault<z.ZodString>;
+}, "strip", z.ZodTypeAny, {
+    index: number[];
+    type: string;
+}, {
+    index: number[];
+    type?: string | undefined;
+}>;
+declare const RegionEntrySchema: z.ZodObject<{
+    index: z.ZodEffects<z.ZodEffects<z.ZodArray<z.ZodEffects<z.ZodTuple<[z.ZodNumber, z.ZodNumber], null>, [number, number], [number, number]>, "many">, [number, number][], [number, number][]>, [number, number][], [number, number][]>;
+    type: z.ZodDefault<z.ZodString>;
+}, "strip", z.ZodTypeAny, {
+    index: [number, number][];
+    type: string;
+}, {
+    index: [number, number][];
+    type?: string | undefined;
+}>;
+declare const FlexEntrySchema: z.ZodObject<{
+    index: z.ZodUnion<[z.ZodEffects<z.ZodEffects<z.ZodArray<z.ZodEffects<z.ZodTuple<[z.ZodNumber, z.ZodNumber], null>, [number, number], [number, number]>, "many">, [number, number][], [number, number][]>, [number, number][], [number, number][]>, z.ZodEffects<z.ZodArray<z.ZodNumber, "many">, number[], number[]>]>;
+    type: z.ZodDefault<z.ZodString>;
+}, "strip", z.ZodTypeAny, {
+    index: number[] | [number, number][];
+    type: string;
+}, {
+    index: number[] | [number, number][];
+    type?: string | undefined;
+}>;
+declare const VariantSchema: z.ZodEffects<z.ZodObject<{
+    position: z.ZodNumber;
+}, "strip", z.ZodUnknown, z.objectOutputType<{
+    position: z.ZodNumber;
+}, z.ZodUnknown, "strip">, z.objectInputType<{
+    position: z.ZodNumber;
+}, z.ZodUnknown, "strip">>, z.objectOutputType<{
+    position: z.ZodNumber;
+}, z.ZodUnknown, "strip">, z.objectInputType<{
+    position: z.ZodNumber;
+}, z.ZodUnknown, "strip">>;
+declare const MetadataSchema: z.ZodObject<{
+    uniprot_id: z.ZodDefault<z.ZodString>;
+    description: z.ZodDefault<z.ZodString>;
+    reference: z.ZodDefault<z.ZodString>;
+    organism: z.ZodDefault<z.ZodString>;
+}, "strict", z.ZodTypeAny, {
+    description: string;
+    uniprot_id: string;
+    reference: string;
+    organism: string;
+}, {
+    description?: string | undefined;
+    uniprot_id?: string | undefined;
+    reference?: string | undefined;
+    organism?: string | undefined;
+}>;
+export declare const A3InputSchema: z.ZodEffects<z.ZodObject<{
+    sequence: z.ZodEffects<z.ZodString, string, string>;
+    annotations: z.ZodDefault<z.ZodObject<{
+        site: z.ZodDefault<z.ZodRecord<z.ZodString, z.ZodObject<{
+            index: z.ZodEffects<z.ZodArray<z.ZodNumber, "many">, number[], number[]>;
+            type: z.ZodDefault<z.ZodString>;
+        }, "strip", z.ZodTypeAny, {
+            index: number[];
+            type: string;
+        }, {
+            index: number[];
+            type?: string | undefined;
+        }>>>;
+        region: z.ZodDefault<z.ZodRecord<z.ZodString, z.ZodObject<{
+            index: z.ZodEffects<z.ZodEffects<z.ZodArray<z.ZodEffects<z.ZodTuple<[z.ZodNumber, z.ZodNumber], null>, [number, number], [number, number]>, "many">, [number, number][], [number, number][]>, [number, number][], [number, number][]>;
+            type: z.ZodDefault<z.ZodString>;
+        }, "strip", z.ZodTypeAny, {
+            index: [number, number][];
+            type: string;
+        }, {
+            index: [number, number][];
+            type?: string | undefined;
+        }>>>;
+        ptm: z.ZodDefault<z.ZodRecord<z.ZodString, z.ZodObject<{
+            index: z.ZodUnion<[z.ZodEffects<z.ZodEffects<z.ZodArray<z.ZodEffects<z.ZodTuple<[z.ZodNumber, z.ZodNumber], null>, [number, number], [number, number]>, "many">, [number, number][], [number, number][]>, [number, number][], [number, number][]>, z.ZodEffects<z.ZodArray<z.ZodNumber, "many">, number[], number[]>]>;
+            type: z.ZodDefault<z.ZodString>;
+        }, "strip", z.ZodTypeAny, {
+            index: number[] | [number, number][];
+            type: string;
+        }, {
+            index: number[] | [number, number][];
+            type?: string | undefined;
+        }>>>;
+        processing: z.ZodDefault<z.ZodRecord<z.ZodString, z.ZodObject<{
+            index: z.ZodUnion<[z.ZodEffects<z.ZodEffects<z.ZodArray<z.ZodEffects<z.ZodTuple<[z.ZodNumber, z.ZodNumber], null>, [number, number], [number, number]>, "many">, [number, number][], [number, number][]>, [number, number][], [number, number][]>, z.ZodEffects<z.ZodArray<z.ZodNumber, "many">, number[], number[]>]>;
+            type: z.ZodDefault<z.ZodString>;
+        }, "strip", z.ZodTypeAny, {
+            index: number[] | [number, number][];
+            type: string;
+        }, {
+            index: number[] | [number, number][];
+            type?: string | undefined;
+        }>>>;
+        variant: z.ZodDefault<z.ZodArray<z.ZodEffects<z.ZodObject<{
+            position: z.ZodNumber;
+        }, "strip", z.ZodUnknown, z.objectOutputType<{
+            position: z.ZodNumber;
+        }, z.ZodUnknown, "strip">, z.objectInputType<{
+            position: z.ZodNumber;
+        }, z.ZodUnknown, "strip">>, z.objectOutputType<{
+            position: z.ZodNumber;
+        }, z.ZodUnknown, "strip">, z.objectInputType<{
+            position: z.ZodNumber;
+        }, z.ZodUnknown, "strip">>, "many">>;
+    }, "strict", z.ZodTypeAny, {
+        variant: z.objectOutputType<{
+            position: z.ZodNumber;
+        }, z.ZodUnknown, "strip">[];
+        region: Record<string, {
+            index: [number, number][];
+            type: string;
+        }>;
+        site: Record<string, {
+            index: number[];
+            type: string;
+        }>;
+        ptm: Record<string, {
+            index: number[] | [number, number][];
+            type: string;
+        }>;
+        processing: Record<string, {
+            index: number[] | [number, number][];
+            type: string;
+        }>;
+    }, {
+        variant?: z.objectInputType<{
+            position: z.ZodNumber;
+        }, z.ZodUnknown, "strip">[] | undefined;
+        region?: Record<string, {
+            index: [number, number][];
+            type?: string | undefined;
+        }> | undefined;
+        site?: Record<string, {
+            index: number[];
+            type?: string | undefined;
+        }> | undefined;
+        ptm?: Record<string, {
+            index: number[] | [number, number][];
+            type?: string | undefined;
+        }> | undefined;
+        processing?: Record<string, {
+            index: number[] | [number, number][];
+            type?: string | undefined;
+        }> | undefined;
+    }>>;
+    metadata: z.ZodDefault<z.ZodObject<{
+        uniprot_id: z.ZodDefault<z.ZodString>;
+        description: z.ZodDefault<z.ZodString>;
+        reference: z.ZodDefault<z.ZodString>;
+        organism: z.ZodDefault<z.ZodString>;
+    }, "strict", z.ZodTypeAny, {
+        description: string;
+        uniprot_id: string;
+        reference: string;
+        organism: string;
+    }, {
+        description?: string | undefined;
+        uniprot_id?: string | undefined;
+        reference?: string | undefined;
+        organism?: string | undefined;
+    }>>;
+}, "strict", z.ZodTypeAny, {
+    metadata: {
+        description: string;
+        uniprot_id: string;
+        reference: string;
+        organism: string;
+    };
+    sequence: string;
+    annotations: {
+        variant: z.objectOutputType<{
+            position: z.ZodNumber;
+        }, z.ZodUnknown, "strip">[];
+        region: Record<string, {
+            index: [number, number][];
+            type: string;
+        }>;
+        site: Record<string, {
+            index: number[];
+            type: string;
+        }>;
+        ptm: Record<string, {
+            index: number[] | [number, number][];
+            type: string;
+        }>;
+        processing: Record<string, {
+            index: number[] | [number, number][];
+            type: string;
+        }>;
+    };
+}, {
+    sequence: string;
+    metadata?: {
+        description?: string | undefined;
+        uniprot_id?: string | undefined;
+        reference?: string | undefined;
+        organism?: string | undefined;
+    } | undefined;
+    annotations?: {
+        variant?: z.objectInputType<{
+            position: z.ZodNumber;
+        }, z.ZodUnknown, "strip">[] | undefined;
+        region?: Record<string, {
+            index: [number, number][];
+            type?: string | undefined;
+        }> | undefined;
+        site?: Record<string, {
+            index: number[];
+            type?: string | undefined;
+        }> | undefined;
+        ptm?: Record<string, {
+            index: number[] | [number, number][];
+            type?: string | undefined;
+        }> | undefined;
+        processing?: Record<string, {
+            index: number[] | [number, number][];
+            type?: string | undefined;
+        }> | undefined;
+    } | undefined;
+}>, {
+    metadata: {
+        description: string;
+        uniprot_id: string;
+        reference: string;
+        organism: string;
+    };
+    sequence: string;
+    annotations: {
+        variant: z.objectOutputType<{
+            position: z.ZodNumber;
+        }, z.ZodUnknown, "strip">[];
+        region: Record<string, {
+            index: [number, number][];
+            type: string;
+        }>;
+        site: Record<string, {
+            index: number[];
+            type: string;
+        }>;
+        ptm: Record<string, {
+            index: number[] | [number, number][];
+            type: string;
+        }>;
+        processing: Record<string, {
+            index: number[] | [number, number][];
+            type: string;
+        }>;
+    };
+}, {
+    sequence: string;
+    metadata?: {
+        description?: string | undefined;
+        uniprot_id?: string | undefined;
+        reference?: string | undefined;
+        organism?: string | undefined;
+    } | undefined;
+    annotations?: {
+        variant?: z.objectInputType<{
+            position: z.ZodNumber;
+        }, z.ZodUnknown, "strip">[] | undefined;
+        region?: Record<string, {
+            index: [number, number][];
+            type?: string | undefined;
+        }> | undefined;
+        site?: Record<string, {
+            index: number[];
+            type?: string | undefined;
+        }> | undefined;
+        ptm?: Record<string, {
+            index: number[] | [number, number][];
+            type?: string | undefined;
+        }> | undefined;
+        processing?: Record<string, {
+            index: number[] | [number, number][];
+            type?: string | undefined;
+        }> | undefined;
+    } | undefined;
+}>;
+export type A3Data = z.infer<typeof A3InputSchema>;
+export type MetadataData = z.infer<typeof MetadataSchema>;
+export type VariantData = z.infer<typeof VariantSchema>;
+export type SiteEntryData = z.infer<typeof SiteEntrySchema>;
+export type RegionEntryData = z.infer<typeof RegionEntrySchema>;
+export type FlexEntryData = z.infer<typeof FlexEntrySchema>;
+export {};
+//# sourceMappingURL=schemas.d.ts.map

package/dist/schemas.d.ts.map

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package/dist/schemas.js

@@ -0,0 +1,131 @@
+import { z } from "zod";
+import { isJsonCompatible, sortDedup, sortRanges } from "./normalize";
+// ── Primitives ────────────────────────────────────────────────────────────────
+// 1-based positive integer position
+const PositionSchema = z.number().int().min(1);
+// Sorted, deduplicated array of positions
+const PositionsSchema = z.array(PositionSchema).transform(sortDedup);
+// Inclusive [start, end] range tuple, start < end
+const RangeTupleSchema = z
+    .tuple([PositionSchema, PositionSchema])
+    .refine(([s, e]) => s < e, { message: "start must be < end" });
+// Sorted array of ranges; overlapping ranges are rejected
+const RangesSchema = z
+    .array(RangeTupleSchema)
+    .transform(sortRanges)
+    .superRefine((ranges, ctx) => {
+    let prev;
+    for (const curr of ranges) {
+        if (prev !== undefined && curr[0] <= prev[1]) {
+            ctx.addIssue({
+                code: z.ZodIssueCode.custom,
+                message: `ranges [${prev[0]},${prev[1]}] and [${curr[0]},${curr[1]}] overlap`,
+            });
+        }
+        prev = curr;
+    }
+});
+// ── Annotation entry schemas ──────────────────────────────────────────────────
+//
+// Canonical form only: { index, type }.
+// Site: always positions. Region: always ranges.
+// PTM / Processing: either positions or ranges (never mixed within one entry).
+// Union order matters — ranges branch is tried first (more specific).
+const SiteEntrySchema = z.object({
+    index: PositionsSchema,
+    type: z.string().default(""),
+});
+const RegionEntrySchema = z.object({
+    index: RangesSchema,
+    type: z.string().default(""),
+});
+const FlexEntrySchema = z.object({
+    index: z.union([RangesSchema, PositionsSchema]),
+    type: z.string().default(""),
+});
+// ── Variant ───────────────────────────────────────────────────────────────────
+// Every variant requires `position`; additional JSON-compatible fields are allowed.
+const VariantSchema = z
+    .object({ position: PositionSchema })
+    .catchall(z.unknown())
+    .refine((v) => isJsonCompatible(v), { message: "variant fields must be JSON-compatible" });
+// ── Annotation families ───────────────────────────────────────────────────────
+const AnnotationsSchema = z
+    .object({
+    site: z.record(z.string().min(1), SiteEntrySchema).default({}),
+    region: z.record(z.string().min(1), RegionEntrySchema).default({}),
+    ptm: z.record(z.string().min(1), FlexEntrySchema).default({}),
+    processing: z.record(z.string().min(1), FlexEntrySchema).default({}),
+    variant: z.array(VariantSchema).default([]),
+})
+    .strict();
+// ── Metadata ──────────────────────────────────────────────────────────────────
+const MetadataSchema = z
+    .object({
+    uniprot_id: z.string().default(""),
+    description: z.string().default(""),
+    reference: z.string().default(""),
+    organism: z.string().default(""),
+})
+    .strict();
+// ── Root schema ───────────────────────────────────────────────────────────────
+export const A3InputSchema = z
+    .object({
+    sequence: z
+        .string()
+        .min(2, "sequence must be at least 2 characters")
+        .regex(/^[A-Za-z*]+$/, "sequence must contain only amino acid letters [A-Za-z] or '*'")
+        .transform((s) => s.toUpperCase()),
+    annotations: AnnotationsSchema.default({
+        site: {},
+        region: {},
+        ptm: {},
+        processing: {},
+        variant: [],
+    }),
+    metadata: MetadataSchema.default({}),
+})
+    .strict()
+    .superRefine((data, ctx) => {
+    const len = data.sequence.length;
+    const boundsMsg = (pos) => `position ${pos} is out of bounds for sequence of length ${len} (must be 1–${len})`;
+    const checkPos = (pos, path) => {
+        if (pos < 1 || pos > len)
+            ctx.addIssue({ code: z.ZodIssueCode.custom, message: boundsMsg(pos), path });
+    };
+    const checkIndex = (index, basePath) => {
+        if (index.length === 0)
+            return;
+        if (Array.isArray(index[0])) {
+            let i = 0;
+            for (const [s, e] of index) {
+                checkPos(s, [...basePath, i, 0]);
+                checkPos(e, [...basePath, i, 1]);
+                i++;
+            }
+        }
+        else {
+            let i = 0;
+            for (const pos of index) {
+                checkPos(pos, [...basePath, i]);
+                i++;
+            }
+        }
+    };
+    for (const [name, entry] of Object.entries(data.annotations.site)) {
+        checkIndex(entry.index, ["annotations", "site", name, "index"]);
+    }
+    for (const [name, entry] of Object.entries(data.annotations.region)) {
+        checkIndex(entry.index, ["annotations", "region", name, "index"]);
+    }
+    for (const [name, entry] of Object.entries(data.annotations.ptm)) {
+        checkIndex(entry.index, ["annotations", "ptm", name, "index"]);
+    }
+    for (const [name, entry] of Object.entries(data.annotations.processing)) {
+        checkIndex(entry.index, ["annotations", "processing", name, "index"]);
+    }
+    data.annotations.variant.forEach((v, i) => {
+        checkPos(v.position, ["annotations", "variant", i, "position"]);
+    });
+});
+//# sourceMappingURL=schemas.js.map

package/dist/schemas.js.map

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package/package.json

@@ -0,0 +1,39 @@
+{
+  "name": "@rtemis/a3",
+  "version": "0.1.0",
+  "description": "Annotated Amino Acid (A3) format — TypeScript implementation",
+  "license": "MPL-2.0",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/rtemis-org/a3",
+    "directory": "typescript"
+  },
+  "type": "module",
+  "exports": {
+    ".": {
+      "import": "./dist/index.js",
+      "types": "./dist/index.d.ts"
+    }
+  },
+  "files": [
+    "dist"
+  ],
+  "sideEffects": false,
+  "publishConfig": {
+    "access": "public"
+  },
+  "scripts": {
+    "build": "tsc -p tsconfig.build.json",
+    "test": "vitest run",
+    "check": "biome check src tests"
+  },
+  "dependencies": {
+    "zod": "^3.23.0"
+  },
+  "devDependencies": {
+    "@biomejs/biome": "^1.9.0",
+    "@types/node": "^25.5.0",
+    "typescript": "^5.5.0",
+    "vitest": "^2.0.0"
+  }
+}