* method
*/
public static final String[] WRITEABLE_FORMATS = new String[]
- { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "AMSA" };
+ { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
+ "AMSA" };
/**
* List of extensions corresponding to file format types in WRITABLE_FNAMES
* that are writable by the application.
*/
public static final String[] WRITABLE_EXTENSIONS = new String[]
- { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar", "sto,stk" };
+ { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
+ "sto,stk" };
/**
* List of writable formats by the application. Order must correspond with the
* WRITABLE_EXTENSIONS list of formats.
*/
public static final String[] WRITABLE_FNAMES = new String[]
- { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview", "STH"};
+ { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
+ "STH" };
/**
* List of readable format file extensions by application in order
System.out.println("Reading file: " + f);
AppletFormatAdapter afa = new AppletFormatAdapter();
String fName = f.getName();
- String extension = fName.substring(fName.lastIndexOf(".") + 1, fName.length());
+ String extension = fName.substring(fName.lastIndexOf(".") + 1,
+ fName.length());
if (extension.equals("stk") || extension.equals("sto"))
- {
- afa.test(f);
+ {
+ afa.test(f);
}
else
{
- Runtime r = Runtime.getRuntime();
- System.gc();
- long memf = -r.totalMemory() + r.freeMemory();
- long t1 = -System.currentTimeMillis();
- Alignment al = afa.readFile(args[i], FILE,
- new IdentifyFile().Identify(args[i], FILE));
- t1 += System.currentTimeMillis();
- System.gc();
- memf += r.totalMemory() - r.freeMemory();
- if (al != null)
- {
- System.out.println("Alignment contains " + al.getHeight()
- + " sequences and " + al.getWidth() + " columns.");
- try
+ Runtime r = Runtime.getRuntime();
+ System.gc();
+ long memf = -r.totalMemory() + r.freeMemory();
+ long t1 = -System.currentTimeMillis();
+ Alignment al = afa.readFile(args[i], FILE,
+ new IdentifyFile().Identify(args[i], FILE));
+ t1 += System.currentTimeMillis();
+ System.gc();
+ memf += r.totalMemory() - r.freeMemory();
+ if (al != null)
{
- System.out.println(new AppletFormatAdapter().formatSequences(
- "FASTA", al, true));
- } catch (Exception e)
+ System.out.println("Alignment contains " + al.getHeight()
+ + " sequences and " + al.getWidth() + " columns.");
+ try
+ {
+ System.out.println(new AppletFormatAdapter()
+ .formatSequences("FASTA", al, true));
+ } catch (Exception e)
+ {
+ System.err
+ .println("Couln't format the alignment for output as a FASTA file.");
+ e.printStackTrace(System.err);
+ }
+ }
+ else
{
- System.err
- .println("Couln't format the alignment for output as a FASTA file.");
- e.printStackTrace(System.err);
+ System.out.println("Couldn't read alignment");
}
- }
- else
- {
- System.out.println("Couldn't read alignment");
- }
- System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
- System.out
- .println("Difference between free memory now and before is "
- + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
+ System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
+ System.out
+ .println("Difference between free memory now and before is "
+ + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
}
} catch (Exception e)
{
System.err.println("Exception when dealing with " + i
+ "'th argument: " + args[i] + "\n" + e);
}
-
+
}
else
{
}
}
- private void test(File f) {
- System.out.println("Reading file: " + f);
- String ff = f.getPath();
- try
- {
- Alignment al = readFile(ff, FILE, new IdentifyFile().Identify(ff, FILE));
- for (int i = 0; i < al.getSequencesArray().length; ++i) {
- al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i));
- }
- AlignFile stFile = new StockholmFile(al);
- stFile.setSeqs(al.getSequencesArray());
-
- String stockholmoutput = stFile.print();
- Alignment al_input = readFile(stockholmoutput, AppletFormatAdapter.PASTE, "STH");
- if (al != null && al_input!= null)
- {
- System.out.println("Alignment contains: " + al.getHeight() + " and " + al_input.getHeight()
- + " sequences; " + al.getWidth() + " and " + al_input.getWidth() + " columns.");
- AlignmentAnnotation[] aa_new = al_input.getAlignmentAnnotation();
- AlignmentAnnotation[] aa_original = al.getAlignmentAnnotation();
-
- // check Alignment annotation
- if (aa_new != null && aa_original != null)
- {
- System.out.println("Alignment contains: " + aa_new.length
- + " and " + aa_original.length + " alignment annotation(s)");
- for (int i = 0; i < aa_original.length; i++)
- {
- if (!equalss(aa_original[i], aa_new[i]))
- System.out.println("Different alignment annotation");
- }
- }
-
- // check sequences, annotation and features
- SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length];
- seq_original = al.getSequencesArray();
- SequenceI[] seq_new = new SequenceI[al_input.getSequencesArray().length];
- seq_new = al_input.getSequencesArray();
- SequenceFeature[] sequenceFeatures_original,sequenceFeatures_new;
- AlignmentAnnotation annot_original, annot_new;
- //
- for (int i = 0; i < al.getSequencesArray().length; i++)
- {
- String name = seq_original[i].getName();
- int start = seq_original[i].getStart();
- int end = seq_original[i].getEnd();
- System.out.println("Check sequence: " + name + "/" + start + "-" + end);
-
- // search equal sequence
- for (int in = 0; in < al_input.getSequencesArray().length; in++) {
- if (name.equals(seq_new[in].getName()) &&
- start == seq_new[in].getStart() &&
- end ==seq_new[in].getEnd())
- {
- String ss_original = seq_original[i].getSequenceAsString();
- String ss_new = seq_new[in].getSequenceAsString();
- if (!ss_original.equals(ss_new))
- {
- System.out.println("The sequences " + name + "/" + start + "-" + end + " are not equal");
- }
-
- // compare sequence features
- if (seq_original[i].getSequenceFeatures() != null && seq_new[in].getSequenceFeatures() != null)
- {
- System.out.println("There are feature!!!");
- sequenceFeatures_original = new SequenceFeature[seq_original[i].getSequenceFeatures().length];
- sequenceFeatures_original = seq_original[i].getSequenceFeatures();
- sequenceFeatures_new = new SequenceFeature[seq_new[in].getSequenceFeatures().length];
- sequenceFeatures_new = seq_new[in].getSequenceFeatures();
-
- if (seq_original[i].getSequenceFeatures().length == seq_new[in].getSequenceFeatures().length)
- {
- for (int feat = 0; feat < seq_original[i].getSequenceFeatures().length; feat++) {
- if (!sequenceFeatures_original[feat].equals(sequenceFeatures_new[feat])) {
- System.out.println("Different features");
- break;
- }
- }
- } else
- {
- System.out.println("different number of features");
- }
- } else if (seq_original[i].getSequenceFeatures() == null && seq_new[in].getSequenceFeatures() == null)
- {
- System.out.println("No sequence features");
- } else if (seq_original[i].getSequenceFeatures() != null && seq_new[in].getSequenceFeatures() == null)
- {
- System.out.println("Coudn't compare sequence features new one");
- }
- // compare alignment annotation
- if (al.getSequenceAt(i).getAnnotation() != null && al_input.getSequenceAt(in).getAnnotation() != null)
- {
- for (int j = 0; j < al.getSequenceAt(i).getAnnotation().length; j++)
- {
- if (al.getSequenceAt(i).getAnnotation()[j] != null &&
- al_input.getSequenceAt(in).getAnnotation()[j] != null)
- {
- annot_original = al.getSequenceAt(i).getAnnotation()[j];
- annot_new = al_input.getSequenceAt(in).getAnnotation()[j];
- if (!equalss(annot_original, annot_new))
- System.out.println("Different annotation");
- }
- }
- } else if (al.getSequenceAt(i).getAnnotation() == null && al_input.getSequenceAt(in).getAnnotation() == null)
- {
- System.out.println("No annotations");
- } else if (al.getSequenceAt(i).getAnnotation() != null && al_input.getSequenceAt(in).getAnnotation() == null)
- {
- System.out.println("Coudn't compare annotations new one");
- }
- break;
- }
- }
- }
- } else
- {
- System.out.println("Couldn't read alignment");
- }
- } catch (Exception e)
- {
- System.err.println("Couln't format the alignment for output file.");
- e.printStackTrace(System.err);
- }
- }
-
- /*
- * compare annotations
- */
- private boolean equalss(AlignmentAnnotation annot_or, AlignmentAnnotation annot_new)
- {
- if (annot_or.annotations.length != annot_new.annotations.length)
- {
- return false;
- }
- for (int i = 0; i < annot_or.annotations.length; i++)
- {
- if (annot_or.annotations[i] != null && annot_new.annotations[i] != null)
- {
- if (!annot_or.annotations[i].displayCharacter.equals(annot_new.annotations[i].displayCharacter) &&
- annot_or.annotations[i].secondaryStructure != annot_new.annotations[i].secondaryStructure &&
- !annot_or.annotations[i].description.equals(annot_new.annotations[i].description))
- {
- return false;
- }
- } else if (annot_or.annotations[i] == null && annot_new.annotations[i] == null)
- {
- continue;
- } else
- {
- return false;
- }
- }
- return true;
- }
+ private void test(File f)
+ {
+ System.out.println("Reading file: " + f);
+ String ff = f.getPath();
+ try
+ {
+ Alignment al = readFile(ff, FILE,
+ new IdentifyFile().Identify(ff, FILE));
+ for (int i = 0; i < al.getSequencesArray().length; ++i)
+ {
+ al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i));
+ }
+ AlignFile stFile = new StockholmFile(al);
+ stFile.setSeqs(al.getSequencesArray());
+
+ String stockholmoutput = stFile.print();
+ Alignment al_input = readFile(stockholmoutput,
+ AppletFormatAdapter.PASTE, "STH");
+ if (al != null && al_input != null)
+ {
+ System.out.println("Alignment contains: " + al.getHeight()
+ + " and " + al_input.getHeight() + " sequences; "
+ + al.getWidth() + " and " + al_input.getWidth()
+ + " columns.");
+ AlignmentAnnotation[] aa_new = al_input.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa_original = al.getAlignmentAnnotation();
+
+ // check Alignment annotation
+ if (aa_new != null && aa_original != null)
+ {
+ System.out.println("Alignment contains: " + aa_new.length
+ + " and " + aa_original.length
+ + " alignment annotation(s)");
+ for (int i = 0; i < aa_original.length; i++)
+ {
+ if (!equalss(aa_original[i], aa_new[i]))
+ System.out.println("Different alignment annotation");
+ }
+ }
+
+ // check sequences, annotation and features
+ SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length];
+ seq_original = al.getSequencesArray();
+ SequenceI[] seq_new = new SequenceI[al_input.getSequencesArray().length];
+ seq_new = al_input.getSequencesArray();
+ SequenceFeature[] sequenceFeatures_original, sequenceFeatures_new;
+ AlignmentAnnotation annot_original, annot_new;
+ //
+ for (int i = 0; i < al.getSequencesArray().length; i++)
+ {
+ String name = seq_original[i].getName();
+ int start = seq_original[i].getStart();
+ int end = seq_original[i].getEnd();
+ System.out.println("Check sequence: " + name + "/" + start + "-"
+ + end);
+
+ // search equal sequence
+ for (int in = 0; in < al_input.getSequencesArray().length; in++)
+ {
+ if (name.equals(seq_new[in].getName())
+ && start == seq_new[in].getStart()
+ && end == seq_new[in].getEnd())
+ {
+ String ss_original = seq_original[i].getSequenceAsString();
+ String ss_new = seq_new[in].getSequenceAsString();
+ if (!ss_original.equals(ss_new))
+ {
+ System.out.println("The sequences " + name + "/" + start
+ + "-" + end + " are not equal");
+ }
+
+ // compare sequence features
+ if (seq_original[i].getSequenceFeatures() != null
+ && seq_new[in].getSequenceFeatures() != null)
+ {
+ System.out.println("There are feature!!!");
+ sequenceFeatures_original = new SequenceFeature[seq_original[i]
+ .getSequenceFeatures().length];
+ sequenceFeatures_original = seq_original[i]
+ .getSequenceFeatures();
+ sequenceFeatures_new = new SequenceFeature[seq_new[in]
+ .getSequenceFeatures().length];
+ sequenceFeatures_new = seq_new[in].getSequenceFeatures();
+
+ if (seq_original[i].getSequenceFeatures().length == seq_new[in]
+ .getSequenceFeatures().length)
+ {
+ for (int feat = 0; feat < seq_original[i]
+ .getSequenceFeatures().length; feat++)
+ {
+ if (!sequenceFeatures_original[feat]
+ .equals(sequenceFeatures_new[feat]))
+ {
+ System.out.println("Different features");
+ break;
+ }
+ }
+ }
+ else
+ {
+ System.out.println("different number of features");
+ }
+ }
+ else if (seq_original[i].getSequenceFeatures() == null
+ && seq_new[in].getSequenceFeatures() == null)
+ {
+ System.out.println("No sequence features");
+ }
+ else if (seq_original[i].getSequenceFeatures() != null
+ && seq_new[in].getSequenceFeatures() == null)
+ {
+ System.out
+ .println("Coudn't compare sequence features new one");
+ }
+ // compare alignment annotation
+ if (al.getSequenceAt(i).getAnnotation() != null
+ && al_input.getSequenceAt(in).getAnnotation() != null)
+ {
+ for (int j = 0; j < al.getSequenceAt(i).getAnnotation().length; j++)
+ {
+ if (al.getSequenceAt(i).getAnnotation()[j] != null
+ && al_input.getSequenceAt(in).getAnnotation()[j] != null)
+ {
+ annot_original = al.getSequenceAt(i).getAnnotation()[j];
+ annot_new = al_input.getSequenceAt(in).getAnnotation()[j];
+ if (!equalss(annot_original, annot_new))
+ System.out.println("Different annotation");
+ }
+ }
+ }
+ else if (al.getSequenceAt(i).getAnnotation() == null
+ && al_input.getSequenceAt(in).getAnnotation() == null)
+ {
+ System.out.println("No annotations");
+ }
+ else if (al.getSequenceAt(i).getAnnotation() != null
+ && al_input.getSequenceAt(in).getAnnotation() == null)
+ {
+ System.out.println("Coudn't compare annotations new one");
+ }
+ break;
+ }
+ }
+ }
+ }
+ else
+ {
+ System.out.println("Couldn't read alignment");
+ }
+ } catch (Exception e)
+ {
+ System.err.println("Couln't format the alignment for output file.");
+ e.printStackTrace(System.err);
+ }
+ }
+
+ /*
+ * compare annotations
+ */
+ private boolean equalss(AlignmentAnnotation annot_or,
+ AlignmentAnnotation annot_new)
+ {
+ if (annot_or.annotations.length != annot_new.annotations.length)
+ {
+ return false;
+ }
+ for (int i = 0; i < annot_or.annotations.length; i++)
+ {
+ if (annot_or.annotations[i] != null
+ && annot_new.annotations[i] != null)
+ {
+ if (!annot_or.annotations[i].displayCharacter
+ .equals(annot_new.annotations[i].displayCharacter)
+ && annot_or.annotations[i].secondaryStructure != annot_new.annotations[i].secondaryStructure
+ && !annot_or.annotations[i].description
+ .equals(annot_new.annotations[i].description))
+ {
+ return false;
+ }
+ }
+ else if (annot_or.annotations[i] == null
+ && annot_new.annotations[i] == null)
+ {
+ continue;
+ }
+ else
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
/**
* try to discover how to access the given file as a valid datasource that
* will be identified as the given type.
{
// static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
StringBuffer out; // output buffer
+
AlignmentI al;
-
+
public StockholmFile()
{
}
/**
- * Creates a new StockholmFile object for output.
- */
+ * Creates a new StockholmFile object for output.
+ */
public StockholmFile(AlignmentI al)
{
this.al = al;
}
-
+
public StockholmFile(String inFile, String type) throws IOException
{
super(inFile, type);
{
// End of the alignment, pass stuff back
this.noSeqs = seqs.size();
-
+
String propety = 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
}
else if (rf.search(dbType))
{
- propety = "RFAM";
+ propety = "RFAM";
}
}
// logger.debug("Number of sequences: " + this.noSeqs);
String desc = (String) accAnnotations.get("DE");
seqO.setDescription((desc == null) ? "" : desc);
}
-
-
-
+
// Add DB References (if any)
if (accAnnotations != null && accAnnotations.containsKey("DR"))
{
String src = dbr.substring(0, dbr.indexOf(";"));
String acn = dbr.substring(dbr.indexOf(";") + 1);
jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);
- }
+ }
}
-
- if (accAnnotations != null && accAnnotations.containsKey("AC") && propety != null)
+
+ if (accAnnotations != null && accAnnotations.containsKey("AC")
+ && propety != null)
{
String dbr = (String) accAnnotations.get("AC");
if (dbr != null)
String src = propety;
String acn = dbr.toString();
jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);
- }
+ }
}
-
-
+
Hashtable features = null;
// We need to adjust the positions of all features to account for gaps
try
// TODO: map coding region to core jalview feature types
String type = i.nextElement().toString();
Hashtable content = (Hashtable) features.remove(type);
-
+
// add alignment annotation for this feature
String key = type2id(type);
- if (key != null)
+ if (key != null)
{
- if (accAnnotations != null && accAnnotations.containsKey(key))
+ if (accAnnotations != null
+ && accAnnotations.containsKey(key))
{
- Vector vv = (Vector) accAnnotations.get(key);
+ Vector vv = (Vector) accAnnotations.get(key);
for (int ii = 0; ii < vv.size(); ii++)
{
- AlignmentAnnotation an = (AlignmentAnnotation) vv.elementAt(ii);
- seqO.addAlignmentAnnotation(an);
- }
+ AlignmentAnnotation an = (AlignmentAnnotation) vv
+ .elementAt(ii);
+ seqO.addAlignmentAnnotation(an);
+ }
}
}
-
+
Enumeration j = content.keys();
while (j.hasMoreElements())
{
convert1 = openparen.replaceAll(annots);
convert2 = closeparen.replaceAll(convert1);
annots = convert2;
-
+
String type = label;
- if (label.contains("_cons")) {
- type = (label.indexOf("_cons") == label.length() - 5) ? label
- .substring(0, label.length() - 5) : label;
- }
+ if (label.contains("_cons"))
+ {
+ type = (label.indexOf("_cons") == label.length() - 5) ? label
+ .substring(0, label.length() - 5) : label;
+ }
boolean ss = false;
type = id2type(type);
if (type.equals("secondary structure"))
}
return annot;
}
-
+
public String print(SequenceI[] s)
{
- // find max length of id
- int max = 0;
- int maxid = 0;
- int in = 0;
- Hashtable dataRef = null;
- while ((in < s.length) && (s[in] != null))
- {
- String tmp = printId(s[in]);
- if (s[in].getSequence().length > max)
- {
- max = s[in].getSequence().length;
- }
-
- if (tmp.length() > maxid)
- {
- maxid = tmp.length();
- }
- if (s[in].getDBRef() != null)
- {
- for (int idb = 0; idb < s[in].getDBRef().length; idb++)
- {
- if (dataRef == null)
- dataRef = new Hashtable();
-
- String datAs1 = s[in].getDBRef()[idb].getSource().toString() + " ; " +s[in].getDBRef()[idb].getAccessionId().toString();
- dataRef.put(tmp, datAs1);
+ // find max length of id
+ int max = 0;
+ int maxid = 0;
+ int in = 0;
+ Hashtable dataRef = null;
+ while ((in < s.length) && (s[in] != null))
+ {
+ String tmp = printId(s[in]);
+ if (s[in].getSequence().length > max)
+ {
+ max = s[in].getSequence().length;
+ }
+
+ if (tmp.length() > maxid)
+ {
+ maxid = tmp.length();
+ }
+ if (s[in].getDBRef() != null)
+ {
+ for (int idb = 0; idb < s[in].getDBRef().length; idb++)
+ {
+ if (dataRef == null)
+ dataRef = new Hashtable();
+
+ String datAs1 = s[in].getDBRef()[idb].getSource().toString()
+ + " ; "
+ + s[in].getDBRef()[idb].getAccessionId().toString();
+ dataRef.put(tmp, datAs1);
+ }
+ }
+ in++;
+ }
+ maxid += 9;
+ int i = 0;
+
+ // output database type
+ if (al.getProperties() != null)
+ {
+ if (!al.getProperties().isEmpty())
+ {
+ Enumeration key = al.getProperties().keys();
+ Enumeration val = al.getProperties().elements();
+ while (key.hasMoreElements())
+ {
+ out.append("#=GF " + key.nextElement() + " " + val.nextElement());
+ out.append(newline);
+ }
+ }
+ }
+
+ // output database accessions
+ if (dataRef != null)
+ {
+ Enumeration en = dataRef.keys();
+ while (en.hasMoreElements())
+ {
+ Object idd = en.nextElement();
+ String type = (String) dataRef.remove(idd);
+ out.append(new Format("%-" + (maxid - 2) + "s").form("#=GS "
+ + idd.toString() + " "));
+ if (type.contains("PFAM") || type.contains("RFAM"))
+ {
+
+ out.append(" AC " + type.substring(type.indexOf(";") + 1));
+ }
+ else
+ {
+ out.append(" DR " + type + " ");
+ }
+ out.append(newline);
+ }
+ }
+
+ // output annotations
+ while (i < s.length && s[i] != null)
+ {
+ if (s[i].getDatasetSequence() != null)
+ {
+ SequenceI ds = s[i].getDatasetSequence();
+ AlignmentAnnotation[] alAnot;
+ Annotation[] ann;
+ Annotation annot;
+ alAnot = s[i].getAnnotation();
+ String feature = "";
+ if (alAnot != null)
+ {
+ for (int j = 0; j < alAnot.length; j++)
+ {
+ if (ds.getSequenceFeatures() != null)
+ {
+ feature = ds.getSequenceFeatures()[0].type;
+ }
+ String key = type2id(feature);
+
+ if (key == null)
+ continue;
+
+ // out.append("#=GR ");
+ out.append(new Format("%-" + maxid + "s").form("#=GR "
+ + printId(s[i]) + " " + key + " "));
+ ann = alAnot[j].annotations;
+ String seq = "";
+ for (int k = 0; k < ann.length; k++)
+ {
+ annot = ann[k];
+ String ch = (annot == null) ? Character.toString(s[i]
+ .getCharAt(k)) : annot.displayCharacter;
+ if (ch.length() == 0)
+ {
+ if (key.equals("SS"))
+ {
+ char ll = annot.secondaryStructure;
+ seq = (Character.toString(ll).equals(" ")) ? seq + "C"
+ : seq + ll;
+ }
+ else
+ {
+ seq += ".";
+ }
+ }
+ else if (ch.length() == 1)
+ {
+ seq += ch;
+ }
+ else if (ch.length() > 1)
+ {
+ seq += ch.charAt(1);
+ }
}
+ out.append(seq);
+ out.append(newline);
}
- in++;
- }
- maxid += 9;
- int i = 0;
-
- // output database type
- if (al.getProperties() != null)
- {
- if (!al.getProperties().isEmpty())
- {
- Enumeration key = al.getProperties().keys();
- Enumeration val = al.getProperties().elements();
- while (key.hasMoreElements())
- {
- out.append("#=GF " + key.nextElement() + " " + val.nextElement());
- out.append(newline);
- }
- }
- }
-
- // output database accessions
- if (dataRef != null)
- {
- Enumeration en = dataRef.keys();
- while (en.hasMoreElements())
- {
- Object idd = en.nextElement();
- String type = (String) dataRef.remove(idd);
- out.append(new Format("%-" + (maxid - 2) + "s").form("#=GS " +idd.toString() + " "));
- if (type.contains("PFAM") || type.contains("RFAM") )
- {
-
- out.append(" AC " + type.substring(type.indexOf(";") + 1));
- } else
- {
- out.append(" DR " + type + " ");
- }
- out.append(newline);
- }
- }
-
- // output annotations
- while (i < s.length && s[i] != null)
- {
- if (s[i].getDatasetSequence() != null)
- {
- SequenceI ds = s[i].getDatasetSequence();
- AlignmentAnnotation[] alAnot;
- Annotation[] ann;
- Annotation annot;
- alAnot = s[i].getAnnotation();
- String feature = "";
- if (alAnot != null)
- {
- for (int j = 0; j < alAnot.length; j++)
- {
- if (ds.getSequenceFeatures() != null)
- {
- feature = ds.getSequenceFeatures()[0].type;
- }
- String key = type2id(feature);
-
-
- if (key == null)
- continue;
-
- // out.append("#=GR ");
- out.append(new Format("%-" + maxid + "s").form("#=GR " + printId(s[i]) + " " + key + " "));
- ann = alAnot[j].annotations;
- String seq = "";
- for (int k = 0; k < ann.length; k++)
- {
- annot = ann[k];
- String ch = (annot == null) ? Character.toString(s[i].getCharAt(k)) : annot.displayCharacter;
- if (ch.length() == 0)
- {
- if (key.equals("SS")) {
- char ll = annot.secondaryStructure;
- seq = (Character.toString(ll).equals(" ")) ? seq + "C" : seq + ll;
- } else {
- seq += ".";
- }
- } else if (ch.length() == 1) {
- seq += ch;
- } else if (ch.length() > 1) {
- seq += ch.charAt(1) ;
- }
- }
- out.append(seq);
- out.append(newline);
- }
- }
- }
-
- out.append(new Format("%-" + maxid + "s").form(printId(s[i])+" "));
- out.append(s[i].getSequenceAsString());
- out.append(newline);
- i++;
- }
-
- // alignment annotation
- AlignmentAnnotation aa;
- if (al.getAlignmentAnnotation() != null)
- {
- for (int ia = 0; ia < al.getAlignmentAnnotation().length; ia++)
- {
- aa = al.getAlignmentAnnotation()[ia];
- if (aa.autoCalculated || !aa.visible)
- {
- continue;
- }
- String seq = "";
- String label;
-
- if (aa.label.equals("seq"))
- label = "seq_cons";
- else
- label = type2id(aa.label.toLowerCase())+"_cons";
-
- if (label == null)
- label = aa.label;
-
- out.append(new Format("%-" + maxid + "s").form("#=GC " + label+" "));
- for (int j = 0; j < aa.annotations.length; j++)
- {
- String ch = (aa.annotations[j] == null) ? "-" : aa.annotations[j].displayCharacter ;
- if (ch.length() == 0)
- {
- char ll = aa.annotations[j].secondaryStructure;
- if (Character.toString(ll).equals(" "))
- seq += "C";
- else
- seq += ll;
- } else if (ch.length() == 1) {
- seq += ch;
- } else if (ch.length() > 1) {
- seq += ch.charAt(1) ;
- }
- }
- out.append(seq);
- out.append(newline);
- }
- }
- return out.toString();
+ }
+ }
+
+ out.append(new Format("%-" + maxid + "s").form(printId(s[i]) + " "));
+ out.append(s[i].getSequenceAsString());
+ out.append(newline);
+ i++;
+ }
+
+ // alignment annotation
+ AlignmentAnnotation aa;
+ if (al.getAlignmentAnnotation() != null)
+ {
+ for (int ia = 0; ia < al.getAlignmentAnnotation().length; ia++)
+ {
+ aa = al.getAlignmentAnnotation()[ia];
+ if (aa.autoCalculated || !aa.visible)
+ {
+ continue;
+ }
+ String seq = "";
+ String label;
+
+ if (aa.label.equals("seq"))
+ label = "seq_cons";
+ else
+ label = type2id(aa.label.toLowerCase()) + "_cons";
+
+ if (label == null)
+ label = aa.label;
+
+ out.append(new Format("%-" + maxid + "s").form("#=GC " + label
+ + " "));
+ for (int j = 0; j < aa.annotations.length; j++)
+ {
+ String ch = (aa.annotations[j] == null) ? "-"
+ : aa.annotations[j].displayCharacter;
+ if (ch.length() == 0)
+ {
+ char ll = aa.annotations[j].secondaryStructure;
+ if (Character.toString(ll).equals(" "))
+ seq += "C";
+ else
+ seq += ll;
+ }
+ else if (ch.length() == 1)
+ {
+ seq += ch;
+ }
+ else if (ch.length() > 1)
+ {
+ seq += ch.charAt(1);
+ }
+ }
+ out.append(seq);
+ out.append(newline);
+ }
+ }
+ return out.toString();
}
public String print()
{
- out = new StringBuffer();
- out.append("# STOCKHOLM 1.0");
- out.append(newline);
+ out = new StringBuffer();
+ out.append("# STOCKHOLM 1.0");
+ out.append(newline);
print(getSeqsAsArray());
-
+
out.append("//");
- out.append(newline);
+ out.append(newline);
return out.toString();
}
+ id);
return id;
}
-
+
protected static String type2id(String type)
{
- String key = null;
- Enumeration e = typeIds.keys();
- while (e.hasMoreElements())
- {
- Object ll = e.nextElement();
- if (typeIds.get(ll).toString().equals(type))
- {
- key = (String) ll;
- break;
- }
- }
- if (key != null)
+ String key = null;
+ Enumeration e = typeIds.keys();
+ while (e.hasMoreElements())
+ {
+ Object ll = e.nextElement();
+ if (typeIds.get(ll).toString().equals(type))
{
- return (String) key;
+ key = (String) ll;
+ break;
}
- System.err.println("Warning : Unknown Stockholm annotation type: "
+ }
+ if (key != null)
+ {
+ return (String) key;
+ }
+ System.err.println("Warning : Unknown Stockholm annotation type: "
+ type);
return key;
}
git://source.jalview.org / jalview.git / commitdiff