/**
* Check whether s qualifier string exists in a StringVector for that qualifier. If the
* StringVector contains the hit, organism, description & e-value then return true.
*
* @param qualStr
* @param qualStringVector
* @return
*/
public static boolean containsStringInStringVector(
final String qualStr, final StringVector qualStringVector) {
StringVector sim1 = StringVector.getStrings(qualStr, ";");
for (int i = 0; i < qualStringVector.size(); i++) {
String thisStr = (String) qualStringVector.get(i);
StringVector sim2 = StringVector.getStrings(thisStr, ";");
// hit
if (!((String) sim1.get(1)).equals((String) sim2.get(1))) continue;
// organism
if (!((String) sim1.get(2)).equals((String) sim2.get(2))) continue;
// description
if (!((String) sim1.get(3)).equals((String) sim2.get(3))) continue;
// e-value
final String evalueString1 = getField("E()=", qualStr);
final String evalueString2 = getField("E()=", thisStr);
if (!(evalueString1.equals(evalueString2))) continue;
return true;
}
return false;
}
/**
* Build a vector of the row data
*
* @param similarityString
* @return
*/
private Vector getRowData(String similarityString, final Vector tableData) {
Vector row = new Vector(NUMBER_COLUMNS);
row.setSize(NUMBER_COLUMNS);
if (similarityString.startsWith("\"")) similarityString = similarityString.substring(1);
if (similarityString.endsWith("\""))
similarityString = similarityString.substring(0, similarityString.length() - 1);
StringVector sim = StringVector.getStrings(similarityString, ";");
// organism
if (sim.size() >= 3) {
int columnIndex = tableData.indexOf(ORGANISM_COL);
row.setElementAt(((String) sim.get(2)).trim(), columnIndex);
}
// hit
if (sim.size() >= 2) {
int columnIndex = tableData.indexOf(HIT_COL);
String hit = ((String) sim.get(1)).trim();
if (hit.startsWith("with=")) hit = hit.substring(5);
final String hits[] = hit.split(" ");
row.setElementAt(hits[0], columnIndex);
if (hits.length > 1) {
// dbxref
columnIndex = tableData.indexOf(HIT_DBXREF_COL);
if (hits[1].startsWith("(") && hits[1].endsWith(")"))
hits[1] = hits[1].substring(1, hits[1].length() - 1);
row.setElementAt(hits[1], columnIndex);
}
}
// description
if (sim.size() >= 4) {
int columnIndex = tableData.indexOf(DESCRIPTION_COL);
row.setElementAt(((String) sim.get(3)).trim(), columnIndex);
}
// e-value
String evalueString;
if (!(evalueString = getField("E()=", similarityString)).equals("")) {
int columnIndex = tableData.indexOf(EVALUE_COL);
row.setElementAt(evalueString, columnIndex);
}
// length
String lenString;
if (!(lenString = getField("length=", similarityString).trim()).equals("")) {
int columnIndex = tableData.indexOf(LENGTH_COL);
row.setElementAt(lenString, columnIndex);
} else if (!(lenString = getField("length", similarityString).trim()).equals("")) {
int columnIndex = tableData.indexOf(LENGTH_COL);
row.setElementAt(lenString, columnIndex);
}
String ungappedId;
if (!(ungappedId = getField("ungapped id", similarityString)).equals("")) {
int columnIndex = tableData.indexOf(ID_COL);
row.setElementAt(ungappedId, columnIndex);
}
String query;
if (!(query = getField("query", similarityString).trim()).equals("")) {
int columnIndex = tableData.indexOf(QUERY_COL);
row.setElementAt(query, columnIndex);
}
String subject;
if (!(subject = getField("subject", similarityString).trim()).equals("")) {
int columnIndex = tableData.indexOf(SUBJECT_COL);
row.setElementAt(subject, columnIndex);
}
String score;
if (!(score = getField("score=", similarityString)).equals("")) {
int columnIndex = tableData.indexOf(SCORE_COL);
row.setElementAt(score, columnIndex);
}
String overlap;
if (!(overlap = getField("overlap=", similarityString)).equals("")) {
int columnIndex = tableData.indexOf(OVERLAP_COL);
row.setElementAt(overlap, columnIndex);
} else if (similarityString.indexOf("overlap;") > -1) {
overlap = null;
for (int i = 0; i < sim.size(); i++) {
String val = (String) sim.get(i);
if (val.endsWith("overlap")) {
overlap = val;
break;
}
}
if (overlap != null) {
int columnIndex = tableData.indexOf(OVERLAP_COL);
row.setElementAt(overlap, columnIndex);
}
}
int columnIndex = tableData.indexOf(METHOD_COL);
row.setElementAt(((String) sim.get(0)).trim(), columnIndex);
return row;
}