private AttributedString getPTMString(Peptide peptide) {
String sequence = peptide.getSequence();
java.util.List<Modification> mods = peptide.getModifications();
AttributedString str = new AttributedString(sequence);
if (mods != null) {
int seqLength = sequence.length();
for (Modification mod : mods) {
int location = mod.getLocation();
location = location == 0 ? 1 : location;
if (seqLength + 1 > location && location > 0) {
str.addAttribute(TextAttribute.FOREGROUND, PTM_COLOR, location - 1, location);
}
}
}
return str;
}
@Override
public void addData(Peptide peptide) {
String sequence = peptide.getSequence();
int seqLength = sequence.length();
List<Modification> mods = peptide.getModifications();
if (mods != null) {
for (Modification mod : mods) {
List<Object> content = new ArrayList<Object>();
// row number
content.add(this.getRowCount() + 1);
// accession
content.add(mod.getAccession());
// name
content.add(mod.getName());
// location
int location = mod.getLocation();
if (location == 0) {
location = 1;
content.add("N Terminal");
} else if (location == seqLength) {
content.add("C Terminal");
} else if (location == -1) {
content.add(null);
} else {
content.add(location + "");
}
// modified residue
if (sequence.length() >= location && location > 0) {
content.add(sequence.charAt(location - 1));
} else {
content.add(null);
}
// mono mass
List<Double> monoMasses = mod.getMonoMassDeltas();
if (monoMasses != null && !monoMasses.isEmpty()) {
content.add(monoMasses.get(0));
} else {
content.add(null);
}
// average mass
List<Double> avgMasses = mod.getAvgMassDeltas();
if (avgMasses != null && !avgMasses.isEmpty()) {
content.add(avgMasses.get(0));
} else {
content.add(null);
}
// ptm database
content.add(mod.getModDatabase());
// ptm database version
content.add(mod.getModDatabaseVersion());
contents.add(content);
}
}
}
private String getToolTipText(java.util.List<Modification> mods, int seqLength) {
StringBuilder tip = new StringBuilder();
if (mods != null && !mods.isEmpty()) {
tip.append("<html>");
for (Modification mod : mods) {
tip.append("<p>");
tip.append("<b><font size=\"3\" color=\"red\">");
tip.append(mod.getAccession());
tip.append("</font></b><br>");
tip.append("<b>Name</b>:");
tip.append(mod.getName());
tip.append("<br>");
tip.append("<b>Location</b>:");
int location = mod.getLocation();
if (location == 0) {
tip.append("N-Terminal");
} else if (location == seqLength) {
tip.append("C-Terminal");
} else {
tip.append(location);
}
tip.append("<br>");
java.util.List<Double> avgs = mod.getAvgMassDeltas();
if (avgs != null) {
for (Double avg : avgs) {
tip.append("<b>Average Mass Delta</b>:");
tip.append(avg);
tip.append("<br>");
}
}
java.util.List<Double> monos = mod.getMonoMassDeltas();
if (monos != null) {
for (Double mono : monos) {
tip.append("<b>Mono Mass Delta</b>:");
tip.append(mono);
tip.append("<br>");
}
}
tip.append("</p>");
tip.append("<br>");
}
tip.append("</html>");
}
return tip.toString();
}