Add /cesymm/:id/fasta route

Author: sbliven

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

@@ -34,4 +34,5 @@ public class BioJavaRoutes {
 	public static String CESYMM_PDB = "/cesymm/:id/pdb";
 	public static String CESYMM_AXES = "/cesymm/:id/axes";
 	public static String CESYMM_TSV = "/cesymm/:id/tsv";
+	public static String CESYMM_FASTA = "/cesymm/:id/fasta";
 }

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

@@ -24,8 +24,11 @@
 
 package org.biojava.http;
 
-import static spark.Spark.*;
+import static spark.Spark.get;
+import static spark.Spark.port;
+import static spark.Spark.staticFileLocation;
 
+import org.biojava.http.compute.CeSymmFastaTransformer;
 import org.biojava.http.compute.CeSymmPDBTransformer;
 import org.biojava.http.compute.CeSymmTSVTransformer;
 import org.biojava.http.compute.JsonTransformer;
@@ -69,5 +72,6 @@ public static void main(String[] args) {
 			};
 		},new CeSymmPDBTransformer());
 		get(BioJavaRoutes.CESYMM_TSV, new CeSymmResultRoute(),new CeSymmTSVTransformer());
+		get(BioJavaRoutes.CESYMM_FASTA, new CeSymmResultRoute(),new CeSymmFastaTransformer());
 	}
 }

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

@@ -0,0 +1,46 @@
+/*
+ *                    BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ *
+ * Created on Jul 20, 2016
+ * Author: blivens 
+ *
+ */
+ 
+package org.biojava.http.compute;
+
+import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
+import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter;
+import org.biojava.nbio.structure.symmetry.internal.CeSymmResult;
+
+import spark.ResponseTransformer;
+ 
+public class CeSymmFastaTransformer implements ResponseTransformer {
+	@Override
+	public String render(Object resultObj) throws Exception {
+		CeSymmResult result = (CeSymmResult) resultObj;
+		MultipleAlignment alignment = result.getMultipleAlignment();
+		if (alignment != null)
+			return MultipleAlignmentWriter.toFASTA(alignment);
+		else {
+			// No alignment; just write header
+			return "";
+		}
+	}
+
+}

src/main/resources/static/index.html

@@ -144,6 +144,14 @@ <h3>CE-Symm</h3>
 			</tr>
 		</table>
 		All aligned residues in the alignment, in tsv format.
+		<table class="route">
+			<tr>
+				<td><pre>/cesymm/:id/fasta</pre></td>
+				<td>Example: <a href="/cesymm/1itb.A/fasta">/cesymm/1itb.A/fasta</a></td>
+			</tr>
+		</table>
+		FASTA format multiple alignment of all repeats. Upper-case letters are aligned.
+		Lower case letters and hyphens are gaps.
 		</p>
 	</div>
 </body>