/*
* getting whole protein sequence from the db ProteinRow
*/
- public List<StructureProteinPrediction> ReadWholeSequence(String queryProtein) {
+ public List<AnnotatedProteinSequenceBean> ReadWholeSequence(String queryProtein) {
final long startTime = System.currentTimeMillis();
String com = "SELECT JobID, Predictions FROM ProteinRow WHERE Protein = '" + queryProtein + "';";
System.out.println("Command: " + com);
List<Row> rows = results.all();
System.out.println("Query time is " + (queryTime - startTime) + " msec");
System.out.println(" rows analysed, " + rows.size());
- List<StructureProteinPrediction> res = new ArrayList<StructureProteinPrediction>();
+ List<AnnotatedProteinSequenceBean> res = new ArrayList<AnnotatedProteinSequenceBean>();
int c = 0;
for (Row r : rows) {
- StructureProteinPrediction structure = new StructureProteinPrediction(queryProtein, r.getString("JobID"), r.getMap(
+ AnnotatedProteinSequenceBean structure = new AnnotatedProteinSequenceBean(queryProtein, r.getString("JobID"), r.getMap(
"Predictions", String.class, String.class));
res.add(structure);
++c;
/*
* getting part of protein sequence from the db ProteinRow
*/
- public List<StructureProteinPrediction> ReadPartOfSequence(String queryProtein) {
+ public List<AnnotatedProteinSequenceBean> ReadPartOfSequence(String queryProtein) {
final long startTime = System.currentTimeMillis();
String com = "SELECT * FROM ProteinRow;";
System.out.println("Command: " + com);
List<Row> rows = results.all();
System.out.println("Query time is " + (queryTime - startTime) + " msec");
System.out.println(" rows analysed, " + rows.size());
- List<StructureProteinPrediction> res = new ArrayList<StructureProteinPrediction>();
+ List<AnnotatedProteinSequenceBean> res = new ArrayList<AnnotatedProteinSequenceBean>();
int c = 0;
for (Row r : rows) {
String prot = r.getString("Protein");
if (prot.matches("(.*)" + queryProtein + "(.*)")) {
- StructureProteinPrediction structure = new StructureProteinPrediction(prot, r.getString("JobID"), r.getMap("Predictions",
+ AnnotatedProteinSequenceBean structure = new AnnotatedProteinSequenceBean(prot, r.getString("JobID"), r.getMap("Predictions",
String.class, String.class));
res.add(structure);
++c;