From 11fa2109fa963fbd910cb127f9161132ec97b9bf Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 5 Feb 2013 15:17:56 +0000 Subject: [PATCH] formatting --- src/jalview/io/AppletFormatAdapter.java | 423 +++++++++++++++------------- src/jalview/io/StockholmFile.java | 459 ++++++++++++++++--------------- 2 files changed, 473 insertions(+), 409 deletions(-) diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index b57b088..f391a54 100755 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@ -45,21 +45,24 @@ public class AppletFormatAdapter * 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 @@ -503,52 +506,53 @@ public class AppletFormatAdapter 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 { @@ -559,160 +563,199 @@ public class AppletFormatAdapter } } - 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. diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index c6a3ce4..ff2b4fa 100644 --- a/src/jalview/io/StockholmFile.java +++ b/src/jalview/io/StockholmFile.java @@ -45,20 +45,21 @@ public class StockholmFile extends AlignFile { // 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); @@ -144,7 +145,7 @@ public class StockholmFile extends AlignFile { // 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 @@ -157,7 +158,7 @@ public class StockholmFile extends AlignFile } else if (rf.search(dbType)) { - propety = "RFAM"; + propety = "RFAM"; } } // logger.debug("Number of sequences: " + this.noSeqs); @@ -202,9 +203,7 @@ public class StockholmFile extends AlignFile String desc = (String) accAnnotations.get("DE"); seqO.setDescription((desc == null) ? "" : desc); } - - - + // Add DB References (if any) if (accAnnotations != null && accAnnotations.containsKey("DR")) { @@ -214,10 +213,11 @@ public class StockholmFile extends AlignFile 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) @@ -225,10 +225,9 @@ public class StockholmFile extends AlignFile 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 @@ -253,22 +252,24 @@ public class StockholmFile extends AlignFile // 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()) { @@ -577,12 +578,13 @@ public class StockholmFile extends AlignFile 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")) @@ -648,192 +650,211 @@ public class StockholmFile extends AlignFile } 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(); } @@ -872,25 +893,25 @@ public class StockholmFile extends AlignFile + 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; } -- 1.7.10.2