import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
+import java.util.Map;
+import java.util.Set;
import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.JpredAlignment;
return "calculating consensus secondary structure prediction using JPred service";
}
- private static HashMap<String, String[]> jpredRowLabels = new HashMap<String, String[]>();
+ private static Map<String, String[]> jpredRowLabels = new HashMap<String, String[]>();
- private static HashSet<String> jpredRes_graph, jpredRes_ssonly;
+ private static final Set<String> jpredRes_graph;
+
+ private static final Set<String> jpredRes_ssonly;
+ static
{
- jpredRes_ssonly = new HashSet();
+ jpredRes_ssonly = new HashSet<String>();
jpredRes_ssonly.add("jnetpred".toLowerCase());
jpredRes_ssonly.add("jnetpssm".toLowerCase());
jpredRes_ssonly.add("jnethmm".toLowerCase());
- jpredRes_graph = new HashSet();
+ jpredRes_graph = new HashSet<String>();
jpredRes_graph.add("jnetconf".toLowerCase());
jpredRes_graph.add("jnet burial".toLowerCase());
}
String[] k = jpredRowLabels.get(fsq.getId());
if (k == null)
{
- k = new String[]
- { fsq.getId(), "JNet Output" };
+ k = new String[] { fsq.getId(), "JNet Output" };
}
if (fsq.getId().startsWith("JNETSOL"))
{
{
sol[spos] = '0';
}
- if (vseq[spos] == 'B' && (sol[spos]=='0' || sol[spos] < amnt))
+ if (vseq[spos] == 'B'
+ && (sol[spos] == '0' || sol[spos] < amnt))
{
sol[spos] = amnt;
}
try
{
elm[i] = new Annotation("" + annot, "" + annot, annot,
- Integer.valueOf(""+annot));
+ Integer.valueOf("" + annot));
} catch (Exception x)
{
System.err.println("Expected numeric value in character '"