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sblivensbliven
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Refactor compute & Add main /cesymm route
1 parent 28c0ae7 commit d9d58b0

14 files changed

Lines changed: 290 additions & 30 deletions

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‎src/main/java/org/biojava/http/BioJavaRoutes.java‎

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@@ -28,5 +28,7 @@ public class BioJavaRoutes {
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public static String PDB = "/pdb/:id";
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public static String MMCIF = "/mmcif/:id";
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public static String NGL = "/ngl/:id";
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public static String CESYMM = "/cesymm/:id";
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public static String CESYMM_JSON = "/cesymm/:id/json";
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public static String CESYMM_PDB = "/cesymm/:id/pdb";
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}

‎src/main/java/org/biojava/http/ServerMain.java‎

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@@ -26,8 +26,10 @@
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import static spark.Spark.get;
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import org.biojava.http.routes.CESymmRoute;
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import org.biojava.http.routes.JsonTransformer;
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import org.biojava.http.compute.CeSymmPDBTransformer;
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import org.biojava.http.compute.JsonTransformer;
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import org.biojava.http.routes.CeSymmResultRoute;
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import org.biojava.http.routes.CeSymmRoute;
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import org.biojava.http.routes.MMCIFRoute;
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import org.biojava.http.routes.NGLRoute;
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import org.biojava.http.routes.PDBRoute;
@@ -50,6 +52,8 @@ public static void main(String[] args) {
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get(BioJavaRoutes.NGL, new NGLRoute(), new HandlebarsTemplateEngine());
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53-
get(BioJavaRoutes.CESYMM_JSON, new CESymmRoute(),new JsonTransformer());
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get(BioJavaRoutes.CESYMM, new CeSymmRoute(), new HandlebarsTemplateEngine());
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get(BioJavaRoutes.CESYMM_JSON, new CeSymmResultRoute(),new JsonTransformer());
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get(BioJavaRoutes.CESYMM_PDB, new CeSymmResultRoute(),new CeSymmPDBTransformer());
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}
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}

‎src/main/java/org/biojava/http/compute/CeSymmPDBTransformer.java‎

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@@ -0,0 +1,64 @@
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/*
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* BioJava development code
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*
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* This code may be freely distributed and modified under the
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* terms of the GNU Lesser General Public Licence. This should
6+
* be distributed with the code. If you do not have a copy,
7+
* see:
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*
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* http://www.gnu.org/copyleft/lesser.html
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*
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* Copyright for this code is held jointly by the individual
12+
* authors. These should be listed in @author doc comments.
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*
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* For more information on the BioJava project and its aims,
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* or to join the biojava-l mailing list, visit the home page
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* at:
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*
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* http://www.biojava.org/
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*
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* Created on Jul 6, 2016
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* Author: blivens
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*
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*/
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package org.biojava.http.compute;
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import java.util.List;
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import org.biojava.nbio.structure.Atom;
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import org.biojava.nbio.structure.Structure;
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import org.biojava.nbio.structure.StructureException;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
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import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentDisplay;
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import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools;
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import org.biojava.nbio.structure.symmetry.internal.CeSymmResult;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import spark.ResponseTransformer;
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public class CeSymmPDBTransformer implements ResponseTransformer {
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public static Logger logger = LoggerFactory.getLogger(CeSymmPDBTransformer.class);
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public CeSymmPDBTransformer() {
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super();
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}
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@Override
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public String render(Object model) {
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CeSymmResult result = (CeSymmResult) model;
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try {
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MultipleAlignment multAln = result.getMultipleAlignment();
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List<Atom[]> rotatedAtoms = MultipleAlignmentDisplay.getRotatedAtoms(multAln );
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Structure artificial = MultipleAlignmentTools.toMultimodelStructure(multAln, rotatedAtoms);
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return artificial.toPDB();
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} catch (StructureException e) {
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logger.error("error rendering CeSymm PDB",e);
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return null;
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}
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}
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}

src/main/java/org/biojava/http/routes/CeSymmResultCache.java renamed to src/main/java/org/biojava/http/compute/CeSymmResultCache.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -22,7 +22,7 @@
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*
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*/
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package org.biojava.http.routes;
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package org.biojava.http.compute;
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import java.util.Collections;
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import java.util.HashMap;

src/main/java/org/biojava/http/routes/CeSymmRunner.java renamed to src/main/java/org/biojava/http/compute/CeSymmRunner.java

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Original file line numberDiff line numberDiff line change
@@ -22,7 +22,7 @@
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*
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*/
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package org.biojava.http.routes;
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package org.biojava.http.compute;
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import java.io.IOException;
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import java.util.concurrent.Callable;

src/main/java/org/biojava/http/routes/JsonTransformer.java renamed to src/main/java/org/biojava/http/compute/JsonTransformer.java

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@@ -22,9 +22,9 @@
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*
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*/
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package org.biojava.http.routes;
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package org.biojava.http.compute;
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import org.biojava.http.json.CESymmResultSerializer;
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import org.biojava.http.json.CeSymmResultSerializer;
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import org.biojava.nbio.structure.symmetry.internal.CeSymmResult;
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import spark.ResponseTransformer;
@@ -39,7 +39,7 @@ public class JsonTransformer implements ResponseTransformer {
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public JsonTransformer() {
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super();
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gson = new GsonBuilder()
42-
.registerTypeAdapter(CeSymmResult.class, new CESymmResultSerializer())
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.registerTypeAdapter(CeSymmResult.class, new CeSymmResultSerializer())
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.create();
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}
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‎src/main/java/org/biojava/http/json/CESymmResultSerializer.java‎

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@@ -36,8 +36,8 @@
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import com.google.gson.JsonSerializationContext;
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import com.google.gson.JsonSerializer;
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public class CESymmResultSerializer implements JsonSerializer<CeSymmResult> {
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private static final Logger logger = LoggerFactory.getLogger(CESymmResultSerializer.class);
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public class CeSymmResultSerializer implements JsonSerializer<CeSymmResult> {
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private static final Logger logger = LoggerFactory.getLogger(CeSymmResultSerializer.class);
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@Override
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public JsonElement serialize(CeSymmResult src, Type typeOfSrc, JsonSerializationContext context) {

‎src/main/java/org/biojava/http/models/CESymmParams.java‎

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Original file line numberDiff line numberDiff line change
@@ -26,12 +26,12 @@
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import org.biojava.nbio.structure.symmetry.internal.CeSymmResult;
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public class CESymmParams {
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public class CeSymmParams {
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3131
private NGLParams ngl;
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private CeSymmResult result;
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public CESymmParams(CeSymmResult result) {
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public CeSymmParams(CeSymmResult result) {
3535
this.result = result;
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this.ngl = new NGLParams("/cesymm/"+result.getStructureId());
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}

‎src/main/java/org/biojava/http/models/CeSymmRouteParams.java‎

Lines changed: 55 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,55 @@
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/*
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* BioJava development code
3+
*
4+
* This code may be freely distributed and modified under the
5+
* terms of the GNU Lesser General Public Licence. This should
6+
* be distributed with the code. If you do not have a copy,
7+
* see:
8+
*
9+
* http://www.gnu.org/copyleft/lesser.html
10+
*
11+
* Copyright for this code is held jointly by the individual
12+
* authors. These should be listed in @author doc comments.
13+
*
14+
* For more information on the BioJava project and its aims,
15+
* or to join the biojava-l mailing list, visit the home page
16+
* at:
17+
*
18+
* http://www.biojava.org/
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*
20+
* Created on Jul 6, 2016
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* Author: blivens
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*
23+
*/
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25+
package org.biojava.http.models;
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27+
28+
public class CeSymmRouteParams extends NGLParams{
29+
private String structureId;
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private String jsonUrl;
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33+
public CeSymmRouteParams(String structureId,String structUrl,String jsonUrl) {
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super(structUrl);
35+
this.structureId = structureId;
36+
this.jsonUrl = jsonUrl;
37+
}
38+
39+
public String getStructureId() {
40+
return structureId;
41+
}
42+
43+
public void setStructureId(String structureId) {
44+
this.structureId = structureId;
45+
}
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public String getJsonUrl() {
48+
return jsonUrl;
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}
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51+
public void setJsonUrl(String jsonUrl) {
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this.jsonUrl = jsonUrl;
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}
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}

‎src/main/java/org/biojava/http/models/NGLParams.java‎

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@@ -49,10 +49,6 @@ public String getStructUrl() {
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public void setStructUrl(String structUrl) {
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this.structUrl = structUrl;
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}
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public String toString() {
54-
return url;
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}
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public int getSize() {
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return size;

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