Merge branch 'master' into PROT-9-webservice

[proteocache.git] / datadb / compbio / cassandra / readers / SequenceReader.java

diff --git a/datadb/compbio/cassandra/readers/SequenceReader.java b/datadb/compbio/cassandra/readers/SequenceReader.java
new file mode 100644 (file)
index 0000000..7e77126
--- /dev/null
+++ b/datadb/compbio/cassandra/readers/SequenceReader.java
@@ -0,0 +1,98 @@
+package compbio.cassandra.readers;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import com.datastax.driver.core.ResultSet;
+import com.datastax.driver.core.Row;
+
+import compbio.beans.ProteinBean;
+
+/**
+ * Reader class for making requests on protein sequences to cassandra.
+ * 
+ * @author Alexander Sherstnev
+ * @author Natasha Sherstneva
+ * 
+ * @since 0.5
+ * @version 1.0 
+ * @since December 2013
+ */
+public class SequenceReader extends CassandraReader {
+
+       public SequenceReader() {
+               super();
+       }
+
+       /**
+        * query: protein sequence
+        * 
+        * @param sequence
+        *            protein sequence or partial of protein sequence
+        * @param searchtype
+        *            "whole" or "partial" of protein sequence
+        * 
+        * @return List<ProteinBean> to the controller SequenceController
+        * 
+        **/
+       public List<ProteinBean> readProteins(String sequence, String searchtype) {
+               List<ProteinBean> query = new ArrayList<ProteinBean>();
+               if (searchtype.equals("whole")) {
+                       ResultSet results = CassandraQuery("SELECT JobID, Predictions FROM ProteinRow WHERE Protein = '" + sequence + "';");
+                       if (results.isExhausted())
+                               return null;
+                       List<Row> rows = results.all();
+                       ProteinBean structure = new ProteinBean(sequence, rows.get(0).getMap("Predictions", String.class, String.class));
+                       for (Row r : rows) {
+                               structure.setJobid(r.getString("JobID"));
+                       }
+                       query.add(structure);
+               } else {
+                       ResultSet results = CassandraQuery("SELECT * FROM ProteinRow;");
+                       if (results.isExhausted())
+                               return null;
+                       List<Row> rows = results.all();
+                       for (Row r : rows) {
+                               String protein = r.getString("Protein");
+                               if (protein.matches("(.*)" + sequence + "(.*)")) {
+                                       ProteinBean foundsequence = new ProteinBean(protein, r.getMap("Predictions", String.class, String.class));
+                                       foundsequence.setJobid(r.getString("JobID"));
+                                       query.add(foundsequence);
+                               }
+                       }
+               }
+               if (searchtype.equals("partial")) {
+                       for (ProteinBean entry : query) {
+                               entry.setSubProt(CreateSubprotein(entry.getSequence(), sequence));
+                       }
+               }
+               return query;
+       }
+
+       /**
+        * create a list of parts of protein sequence for highlighting current value
+        * in report;
+        * 
+        * @param protein
+        *            protein sequence
+        * @param subprot
+        *            partial of protein sequence
+        * 
+        * @return List<String>
+        * 
+        **/
+       private static List<String> CreateSubprotein(String protein, String subprot) {
+               List<String> sub = new ArrayList<String>();
+               String subStr = protein;
+               while (subStr.length() > 0 && subStr.contains(subprot)) {
+                       String first = subStr.substring(0, subStr.indexOf(subprot));
+                       if (first.length() > 0)
+                               sub.add(first);
+                       sub.add(subprot);
+                       subStr = subStr.substring(subStr.indexOf(subprot) + subprot.length(), subStr.length());
+               }
+               if (subStr.length() > 0)
+                       sub.add(subStr);
+               return sub;
+       }
+}