{
private static final String ANNOTATION = "annotation";
- private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
-
- private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
+// private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
+//
+// private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
public static final Regex DETECT_BRACKETS = new Regex(
"(<|>|\\[|\\]|\\(|\\)|\\{|\\})");
- public static final String RNASS_BRACKETS = "<>[]() {}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz";
+ // WUSS extended symbols. Avoid ambiguity with protein SS annotations by using NOT_RNASS first.
+ public static final String RNASS_BRACKETS = "<>[](){}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz";
+
+ // use the following regex to decide an annotations (whole) line is NOT an RNA
+ // SS (it contains only E,H,e,h and other non-brace/non-alpha chars)
+ private static final Regex NOT_RNASS = new Regex(
+ "^[^<>[\\](){}A-DF-Za-df-z]*$");
StringBuffer out; // output buffer
Regex openparen = new Regex("(<|\\[)", "(");
Regex closeparen = new Regex("(>|\\])", ")");
- // Detect if file is RNA by looking for bracket types
- Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
+// // Detect if file is RNA by looking for bracket types
+// Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
rend.optimize();
p.optimize();
// End of the alignment, pass stuff back
this.noSeqs = seqs.size();
- String seqdb, dbsource = null;
+ String dbsource = null;
Regex pf = new Regex("PF[0-9]{5}(.*)"); // Finds AC for Pfam
Regex rf = new Regex("RF[0-9]{5}(.*)"); // Finds AC for Rfam
if (getAlignmentProperty("AC") != null)
// convert1 = OPEN_PAREN.replaceAll(annots);
// convert2 = CLOSE_PAREN.replaceAll(convert1);
// annots = convert2;
-
- // DEBUG
- System.out.println(
- "*** parseAnnotationRow called with\n annotation='"
- + annotation + "'\n label='" + label
- + "'\n annots='" + annots + "'");
String type = label;
if (label.contains("_cons"))
if (type.equalsIgnoreCase("secondary structure"))
{
ss = true;
- isrnass = DETECT_BRACKETS.search(annots);
+ isrnass = !NOT_RNASS.search(annots); // sorry about the double negative
+ // here (it's easier for dealing with
+ // other non-alpha-non-brace chars)
}
if (type.equalsIgnoreCase("posterior probability"))
{
int max = 0;
int maxid = 0;
int in = 0;
- Hashtable dataRef = null;
- while ((in < s.length) && (s[in] != null))
+ int slen = s.length;
+ SequenceI seq;
+ Hashtable<String, String> dataRef = null;
+ while ((in < slen) && ((seq = s[in]) != null))
{
- String tmp = printId(s[in], jvSuffix);
- max = Math.max(max, s[in].getLength());
+ String tmp = printId(seq, jvSuffix);
+ max = Math.max(max, seq.getLength());
if (tmp.length() > maxid)
{
maxid = tmp.length();
}
- if (s[in].getDBRefs() != null)
+ List<DBRefEntry> seqrefs = seq.getDBRefs();
+ int ndb;
+ if (seqrefs != null && (ndb = seqrefs.size()) > 0)
{
- for (int idb = 0; idb < s[in].getDBRefs().length; idb++)
+ if (dataRef == null)
+ {
+ dataRef = new Hashtable<>();
+ }
+ for (int idb = 0; idb < ndb; idb++)
{
- if (dataRef == null)
- {
- dataRef = new Hashtable();
- }
- String datAs1 = s[in].getDBRefs()[idb].getSource().toString()
+ DBRefEntry ref = seqrefs.get(idb);
+ String datAs1 = ref.getSource().toString()
+ " ; "
- + s[in].getDBRefs()[idb].getAccessionId().toString();
+ + ref.getAccessionId().toString();
dataRef.put(tmp, datAs1);
}
}
// output database accessions
if (dataRef != null)
{
- Enumeration en = dataRef.keys();
+ Enumeration<String> en = dataRef.keys();
while (en.hasMoreElements())
{
Object idd = en.nextElement();
}
// output annotations
- while (i < s.length && s[i] != null)
+ while (i < slen && (seq = s[i]) != null)
{
- AlignmentAnnotation[] alAnot = s[i].getAnnotation();
+ AlignmentAnnotation[] alAnot = seq.getAnnotation();
if (alAnot != null)
{
Annotation[] ann;
- for (int j = 0; j < alAnot.length; j++)
+ for (int j = 0, nj = alAnot.length; j < nj; j++)
{
String key = type2id(alAnot[j].label);
boolean isrna = alAnot[j].isValidStruc();
- // bs debug
- System.out.println("SEQUENCE " + i + "/" + s.length + " ISRNA="
- + isrna + ".");
+
if (isrna)
{
// hardwire to secondary structure if there is RNA secondary
// out.append("#=GR ");
out.append(new Format("%-" + maxid + "s").form(
- "#=GR " + printId(s[i], jvSuffix) + " " + key + " "));
+ "#=GR " + printId(seq, jvSuffix) + " " + key + " "));
ann = alAnot[j].annotations;
- String seq = "";
- for (int k = 0; k < ann.length; k++)
+ String sseq = "";
+ for (int k = 0, nk = ann.length; k < nk; k++)
{
- seq += outputCharacter(key, k, isrna, ann, s[i]);
+ sseq += outputCharacter(key, k, isrna, ann, seq);
}
- // bs debug
- System.out.println("APPENDING SEQ: KEY=" + key + " ISRNA=" + isrna
- + ".\n" + "SEQ=" + seq + "\n");
- out.append(seq);
+ out.append(sseq);
out.append(newline);
}
}
out.append(new Format("%-" + maxid + "s")
- .form(printId(s[i], jvSuffix) + " "));
- out.append(s[i].getSequenceAsString());
- // bs debug
- System.out.println("ALSO APPENDING " + s[i].getSequenceAsString());
+ .form(printId(seq, jvSuffix) + " "));
+ out.append(seq.getSequenceAsString());
out.append(newline);
i++;
}
// alignment annotation
AlignmentAnnotation aa;
- if (al.getAlignmentAnnotation() != null)
+ AlignmentAnnotation[] an = al.getAlignmentAnnotation();
+ if (an != null)
{
- for (int ia = 0; ia < al.getAlignmentAnnotation().length; ia++)
+ for (int ia = 0, na = an.length; ia < na; ia++)
{
- aa = al.getAlignmentAnnotation()[ia];
+ aa = an[ia];
if (aa.autoCalculated || !aa.visible || aa.sequenceRef != null)
{
continue;
}
- String seq = "";
+ String sseq = "";
String label;
String key = "";
if (aa.label.equals("seq"))
out.append(
new Format("%-" + maxid + "s").form("#=GC " + label + " "));
boolean isrna = aa.isValidStruc();
- for (int j = 0; j < aa.annotations.length; j++)
+ for (int j = 0, nj = aa.annotations.length; j < nj; j++)
{
- seq += outputCharacter(key, j, isrna, aa.annotations, null);
+ sseq += outputCharacter(key, j, isrna, aa.annotations, null);
}
-
- // bs debug
- System.out.println(
- "PRINTING SEQ: KEY=" + key + " ISRNA=" + isrna + ".\n"
- + "SEQ=" + seq + "\n");
-
- out.append(seq);
+ out.append(sseq);
out.append(newline);
}
}
String ch = (annot == null)
? ((sequenceI == null) ? "-"
: Character.toString(sequenceI.getCharAt(k)))
- : annot.displayCharacter;
+ : (annot.displayCharacter == null
+ ? String.valueOf(annot.secondaryStructure)
+ : annot.displayCharacter);
+ if (ch == null)
+ {
+ ch = " ";
+ }
if (key != null && key.equals("SS"))
{
char ssannotchar = ' ';
}
if (charset)
{
- if (ssannotchar == ' ' && isrna)
- {
- ssannotchar = '.';
- }
- return ssannotchar;
+ return (ssannotchar == ' ' && isrna) ? '.' : ssannotchar;
}
}