import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;\r
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;\r
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;\r
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;\r
+import fr.orsay.lri.varna.factories.RNAFactory;\r
+import fr.orsay.lri.varna.models.rna.RNA;\r
import jalview.datamodel.*;\r
import jalview.analysis.Rna;\r
\r
public class StockholmFile extends AlignFile\r
{\r
// static Logger logger = Logger.getLogger("jalview.io.StockholmFile");\r
-\r
+ protected ArrayList<RNA> result;\r
+ public String id;\r
+ \r
public StockholmFile()\r
{\r
}\r
\r
- public StockholmFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException\r
+ public StockholmFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses\r
{\r
super(inFile, type);\r
}\r
\r
- public StockholmFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException\r
+ public StockholmFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses\r
{\r
super(source);\r
}\r
* \r
* @throws IOException\r
* If there is an error with the input file\r
+ * @throws ExceptionUnmatchedClosingParentheses \r
*/\r
- public void parse() throws IOException\r
+ public void parse() throws IOException, ExceptionUnmatchedClosingParentheses\r
{\r
- StringBuffer treeString = new StringBuffer();\r
- String treeName = null;\r
- // --------------- Variable Definitions -------------------\r
- String line;\r
- String version;\r
- // String id;\r
- Hashtable seqAnn = new Hashtable(); // Sequence related annotations\r
- Hashtable seqs = new Hashtable();\r
- Regex p, r, rend, s, x;\r
-\r
- // Temporary line for processing RNA annotation\r
- // String RNAannot = "";\r
-\r
- // ------------------ Parsing File ----------------------\r
- // First, we have to check that this file has STOCKHOLM format, i.e. the\r
- // first line must match\r
- r = new Regex("# STOCKHOLM ([\\d\\.]+)");\r
- if (!r.search(nextLine()))\r
- {\r
- throw new IOException(\r
- "This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'");\r
- }\r
- else\r
- {\r
- version = r.stringMatched(1);\r
- // logger.debug("Stockholm version: " + version);\r
- }\r
-\r
- // We define some Regexes here that will be used regularily later\r
- rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment\r
- p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in\r
- // id/from/to\r
- s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype\r
- r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line\r
- x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence\r
-\r
- // Convert all bracket types to parentheses (necessary for passing to VARNA)\r
- Regex openparen = new Regex("(<|\\[)", "(");\r
- Regex closeparen = new Regex("(>|\\])", ")");\r
-\r
- // Detect if file is RNA by looking for bracket types\r
- Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");\r
-\r
- rend.optimize();\r
- p.optimize();\r
- s.optimize();\r
- r.optimize();\r
- x.optimize();\r
- openparen.optimize();\r
- closeparen.optimize();\r
-\r
- while ((line = nextLine()) != null)\r
- {\r
- if (line.length() == 0)\r
- {\r
- continue;\r
- }\r
- if (rend.search(line))\r
- {\r
- // End of the alignment, pass stuff back\r
-\r
- this.noSeqs = seqs.size();\r
- // logger.debug("Number of sequences: " + this.noSeqs);\r
- Enumeration accs = seqs.keys();\r
- while (accs.hasMoreElements())\r
- {\r
- String acc = (String) accs.nextElement();\r
- // logger.debug("Processing sequence " + acc);\r
- String seq = (String) seqs.remove(acc);\r
- if (maxLength < seq.length())\r
- {\r
- maxLength = seq.length();\r
- }\r
- int start = 1;\r
- int end = -1;\r
- String sid = acc;\r
- /*\r
- * Retrieve hash of annotations for this accession\r
- * Associate Annotation with accession\r
- */\r
- Hashtable accAnnotations = null;\r
-\r
- if (seqAnn != null && seqAnn.containsKey(acc))\r
- {\r
- accAnnotations = (Hashtable) seqAnn.remove(acc);\r
- //TODO: add structures to sequence\r
- }\r
-\r
- // Split accession in id and from/to\r
- if (p.search(acc))\r
- {\r
- sid = p.stringMatched(1);\r
- start = Integer.parseInt(p.stringMatched(2));\r
- end = Integer.parseInt(p.stringMatched(3));\r
- }\r
- // logger.debug(sid + ", " + start + ", " + end);\r
-\r
- Sequence seqO = new Sequence(sid, seq, start, end);\r
- // Add Description (if any)\r
- if (accAnnotations != null && accAnnotations.containsKey("DE"))\r
- {\r
- String desc = (String) accAnnotations.get("DE");\r
- seqO.setDescription((desc == null) ? "" : desc);\r
- }\r
- // Add DB References (if any)\r
- if (accAnnotations != null && accAnnotations.containsKey("DR"))\r
- {\r
- String dbr = (String) accAnnotations.get("DR");\r
- if (dbr != null && dbr.indexOf(";") > -1)\r
- {\r
- String src = dbr.substring(0, dbr.indexOf(";"));\r
- String acn = dbr.substring(dbr.indexOf(";") + 1);\r
- jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);\r
- // seqO.addDBRef(dbref);\r
- }\r
- } \r
- if (accAnnotations != null && accAnnotations.containsKey("SS"))\r
- {\r
- Vector v = (Vector) accAnnotations.get("SS");\r
- \r
- for (int i = 0; i < v.size(); i++)\r
- {\r
- AlignmentAnnotation an = (AlignmentAnnotation) v.elementAt(i);\r
- seqO.addAlignmentAnnotation(an);\r
- //annotations.add(an);\r
- }\r
- }\r
- \r
- Hashtable features = null;\r
- // We need to adjust the positions of all features to account for gaps\r
- try\r
- {\r
- features = (Hashtable) accAnnotations.remove("features");\r
- } catch (java.lang.NullPointerException e)\r
- {\r
- // loggerwarn("Getting Features for " + acc + ": " +\r
- // e.getMessage());\r
- // continue;\r
- }\r
- // if we have features\r
- if (features != null)\r
- {\r
- int posmap[] = seqO.findPositionMap();\r
- Enumeration i = features.keys();\r
- while (i.hasMoreElements())\r
- {\r
- // TODO: parse out secondary structure annotation as annotation\r
- // row\r
- // TODO: parse out scores as annotation row\r
- // TODO: map coding region to core jalview feature types\r
- String type = i.nextElement().toString();\r
- Hashtable content = (Hashtable) features.remove(type);\r
- Enumeration j = content.keys();\r
- while (j.hasMoreElements())\r
- {\r
- String desc = j.nextElement().toString();\r
- String ns = content.get(desc).toString();\r
- char[] byChar = ns.toCharArray();\r
- for (int k = 0; k < byChar.length; k++)\r
- {\r
- char c = byChar[k];\r
- if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM\r
- // uses\r
- // '.'\r
- // for\r
- // feature\r
- // background\r
- {\r
- int new_pos = posmap[k]; // look up nearest seqeunce\r
- // position to this column\r
- SequenceFeature feat = new SequenceFeature(type, desc,\r
- new_pos, new_pos, 0f, null);\r
-\r
- seqO.addSequenceFeature(feat);\r
- }\r
- }\r
- }\r
-\r
- }\r
-\r
- }\r
- // garbage collect\r
-\r
- // logger.debug("Adding seq " + acc + " from " + start + " to " + end\r
- // + ": " + seq);\r
- this.seqs.addElement(seqO);\r
- }\r
- return; // finished parsing this segment of source\r
- }\r
- else if (!r.search(line))\r
- {\r
- // System.err.println("Found sequence line: " + line);\r
-\r
- // Split sequence in sequence and accession parts\r
- if (!x.search(line))\r
- {\r
- // logger.error("Could not parse sequence line: " + line);\r
- throw new IOException("Could not parse sequence line: " + line);\r
- }\r
- String ns = (String) seqs.get(x.stringMatched(1));\r
- if (ns == null)\r
- {\r
- ns = "";\r
- }\r
- ns += x.stringMatched(2);\r
-\r
- seqs.put(x.stringMatched(1), ns);\r
- }\r
- else\r
- {\r
- String annType = r.stringMatched(1);\r
- String annContent = r.stringMatched(2);\r
-\r
- // System.err.println("type:" + annType + " content: " + annContent);\r
-\r
- if (annType.equals("GF"))\r
- {\r
- /*\r
- * Generic per-File annotation, free text Magic features: #=GF NH\r
- * <tree in New Hampshire eXtended format> #=GF TN <Unique identifier\r
- * for the next tree> Pfam descriptions: 7. DESCRIPTION OF FIELDS\r
- * \r
- * Compulsory fields: ------------------\r
- * \r
- * AC Accession number: Accession number in form PFxxxxx.version or\r
- * PBxxxxxx. ID Identification: One word name for family. DE\r
- * Definition: Short description of family. AU Author: Authors of the\r
- * entry. SE Source of seed: The source suggesting the seed members\r
- * belong to one family. GA Gathering method: Search threshold to\r
- * build the full alignment. TC Trusted Cutoff: Lowest sequence score\r
- * and domain score of match in the full alignment. NC Noise Cutoff:\r
- * Highest sequence score and domain score of match not in full\r
- * alignment. TP Type: Type of family -- presently Family, Domain,\r
- * Motif or Repeat. SQ Sequence: Number of sequences in alignment. AM\r
- * Alignment Method The order ls and fs hits are aligned to the model\r
- * to build the full align. // End of alignment.\r
- * \r
- * Optional fields: ----------------\r
- * \r
- * DC Database Comment: Comment about database reference. DR Database\r
- * Reference: Reference to external database. RC Reference Comment:\r
- * Comment about literature reference. RN Reference Number: Reference\r
- * Number. RM Reference Medline: Eight digit medline UI number. RT\r
- * Reference Title: Reference Title. RA Reference Author: Reference\r
- * Author RL Reference Location: Journal location. PI Previous\r
- * identifier: Record of all previous ID lines. KW Keywords: Keywords.\r
- * CC Comment: Comments. NE Pfam accession: Indicates a nested domain.\r
- * NL Location: Location of nested domains - sequence ID, start and\r
- * end of insert.\r
- * \r
- * Obsolete fields: ----------- AL Alignment method of seed: The\r
- * method used to align the seed members.\r
- */\r
- // Let's save the annotations, maybe we'll be able to do something\r
- // with them later...\r
- Regex an = new Regex("(\\w+)\\s*(.*)");\r
- if (an.search(annContent))\r
- {\r
- if (an.stringMatched(1).equals("NH"))\r
- {\r
- treeString.append(an.stringMatched(2));\r
- }\r
- else if (an.stringMatched(1).equals("TN"))\r
- {\r
- if (treeString.length() > 0)\r
- {\r
- if (treeName == null)\r
- {\r
- treeName = "Tree " + (getTreeCount() + 1);\r
- }\r
- addNewickTree(treeName, treeString.toString());\r
- }\r
- treeName = an.stringMatched(2);\r
- treeString = new StringBuffer();\r
- }\r
- setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));\r
- }\r
- }\r
- else if (annType.equals("GS"))\r
- {\r
- // Generic per-Sequence annotation, free text\r
- /*\r
- * Pfam uses these features: Feature Description ---------------------\r
- * ----------- AC <accession> ACcession number DE <freetext>\r
- * DEscription DR <db>; <accession>; Database Reference OS <organism>\r
- * OrganiSm (species) OC <clade> Organism Classification (clade, etc.)\r
- * LO <look> Look (Color, etc.)\r
- */\r
- if (s.search(annContent))\r
- {\r
- String acc = s.stringMatched(1);\r
- String type = s.stringMatched(2);\r
- String content = s.stringMatched(3);\r
- // TODO: store DR in a vector.\r
- // TODO: store AC according to generic file db annotation.\r
- Hashtable ann;\r
- if (seqAnn.containsKey(acc))\r
- {\r
- ann = (Hashtable) seqAnn.get(acc);\r
- }\r
- else\r
- {\r
- ann = new Hashtable();\r
- }\r
- ann.put(type, content);\r
- seqAnn.put(acc, ann);\r
- }\r
- else\r
- {\r
- throw new IOException("Error parsing " + line);\r
- }\r
- }\r
- else if (annType.equals("GC"))\r
- {\r
- // Generic per-Column annotation, exactly 1 char per column\r
- // always need a label.\r
- if (x.search(annContent))\r
- {\r
- // parse out and create alignment annotation directly.\r
- parseAnnotationRow(annotations, x.stringMatched(1),\r
- x.stringMatched(2));\r
- }\r
- }\r
- else if (annType.equals("GR"))\r
- {\r
- // Generic per-Sequence AND per-Column markup, exactly 1 char per\r
- // column\r
- /*\r
- * Feature Description Markup letters ------- -----------\r
- * -------------- SS Secondary Structure [HGIEBTSCX] SA Surface\r
- * Accessibility [0-9X] (0=0%-10%; ...; 9=90%-100%) TM TransMembrane\r
- * [Mio] PP Posterior Probability [0-9*] (0=0.00-0.05; 1=0.05-0.15;\r
- * *=0.95-1.00) LI LIgand binding [*] AS Active Site [*] IN INtron (in\r
- * or after) [0-2]\r
- */\r
- if (s.search(annContent))\r
- {\r
- String acc = s.stringMatched(1);\r
- String type = s.stringMatched(2);\r
- String seq = new String(s.stringMatched(3));\r
- String description = null;\r
- // Check for additional information about the current annotation\r
- // We use a simple string tokenizer here for speed\r
- StringTokenizer sep = new StringTokenizer(seq, " \t");\r
- description = sep.nextToken();\r
- if (sep.hasMoreTokens())\r
- {\r
- seq = sep.nextToken();\r
- }\r
- else\r
- {\r
- seq = description;\r
- description = new String();\r
- }\r
- // sequence id with from-to fields\r
-\r
- Hashtable ann;\r
- // Get an object with all the annotations for this sequence\r
- if (seqAnn.containsKey(acc))\r
- {\r
- // logger.debug("Found annotations for " + acc);\r
- ann = (Hashtable) seqAnn.get(acc);\r
- }\r
- else\r
- {\r
- // logger.debug("Creating new annotations holder for " + acc);\r
- ann = new Hashtable();\r
- seqAnn.put(acc, ann);\r
- }\r
- //TODO test structure, call parseAnnotationRow with vector from hashtable for specific sequence\r
- Hashtable features;\r
- // Get an object with all the content for an annotation\r
- if (ann.containsKey("features"))\r
- {\r
- // logger.debug("Found features for " + acc);\r
- features = (Hashtable) ann.get("features");\r
- }\r
- else\r
- {\r
- // logger.debug("Creating new features holder for " + acc);\r
- features = new Hashtable();\r
- ann.put("features", features);\r
- }\r
-\r
- Hashtable content;\r
- if (features.containsKey(this.id2type(type)))\r
- {\r
- // logger.debug("Found content for " + this.id2type(type));\r
- content = (Hashtable) features.get(this.id2type(type));\r
- }\r
- else\r
- {\r
- // logger.debug("Creating new content holder for " +\r
- // this.id2type(type));\r
- content = new Hashtable();\r
- features.put(this.id2type(type), content);\r
- }\r
- String ns = (String) content.get(description);\r
- if (ns == null)\r
- {\r
- ns = "";\r
- }\r
- ns += seq;\r
- content.put(description, ns);\r
-
- if(type.equals("SS")){\r
- Hashtable strucAnn;\r
- if (seqAnn.containsKey(acc))\r
- {\r
- strucAnn = (Hashtable) seqAnn.get(acc);\r
- }\r
- else\r
- {\r
- strucAnn = new Hashtable();\r
- }\r
- \r
- Vector newStruc=new Vector();\r
- parseAnnotationRow(newStruc, type,ns);\r
- \r
- strucAnn.put(type, newStruc);\r
- seqAnn.put(acc, strucAnn);\r
- }\r
- }\r
- else\r
- {\r
- System.err\r
- .println("Warning - couldn't parse sequence annotation row line:\n"\r
- + line);\r
- // throw new IOException("Error parsing " + line);\r
- }\r
- }\r
- else\r
- {\r
- throw new IOException("Unknown annotation detected: " + annType\r
- + " " + annContent);\r
- }\r
- }\r
- }\r
- if (treeString.length() > 0)\r
- {\r
- if (treeName == null)\r
- {\r
- treeName = "Tree " + (1 + getTreeCount());\r
- }\r
- addNewickTree(treeName, treeString.toString());\r
- }\r
+ FileReader fr = null;\r
+ fr = new FileReader(inFile); \r
+\r
+ BufferedReader r = new BufferedReader (fr);\r
+ result = RNAFactory.loadSecStrStockholm(r);\r
+ System.out.println("this is the secondary scructure:" +result.size());\r
+ SequenceI[] seqs = new SequenceI[result.size()];\r
+ System.out.println(type); //the type is "File"\r
+ System.out.println(inFile );//inFile is the path\r
+ for(int i=0;i<result.size();i++)\r
+ {\r
+ RNA current = result.get(i);\r
+ \r
+ System.out.println(current.getSeq());\r
+ //System.out.println(result.get(i).getStructBPSEQ());\r
+ System.out.println(result.get(i).getStructDBN(true));\r
+ System.out.println(i);\r
+ String rna =current.getStructDBN(true);\r
+ String seq = current.getSeq();\r
+ int begin=0;\r
+ int end = seq.length()-1;\r
+ id = safeName(getDataName());\r
+ seqs[i] = new Sequence(id, seq, begin, end);\r
+ String[] annot=new String[rna.length()] ;\r
+ Annotation[] ann = new Annotation[rna.length()];\r
+ for(int j=0;j<rna.length();j++)\r
+ {\r
+ annot[j] =rna.substring(j,j+1);\r
+ \r
+ }\r
+ \r
+ for(int k=0;k<rna.length();k++)\r
+ {\r
+ ann[k] = new Annotation(annot[k], "", jalview.schemes.ResidueProperties.getRNASecStrucState(annot[k]).charAt(0), 0f);\r
+ \r
+ }\r
+ AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",current.getID(),ann);\r
+ \r
+ seqs[i].addAlignmentAnnotation(align);\r
+ seqs[i].setRNA(result.get(i));\r
+ this.annotations.addElement(align);\r
+ }\r
+ this.setSeqs(seqs);\r
+ \r
}\r
-\r
+// r = new Regex("# STOCKHOLM ([\\d\\.]+)");\r
+ // if (!r.search(nextLine()))\r
+// {\r
+// throw new IOException(\r
+// "This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'");\r
+// }\r
+// else\r
+// {\r
+// version = r.stringMatched(1);\r
+// // logger.debug("Stockholm version: " + version);\r
+// }\r
+//\r
+// // We define some Regexes here that will be used regularily later\r
+// rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment\r
+// p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in\r
+// // id/from/to\r
+// s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype\r
+// r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line\r
+// x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence\r
+//\r
+// // Convert all bracket types to parentheses (necessary for passing to VARNA)\r
+// Regex openparen = new Regex("(<|\\[)", "(");\r
+// Regex closeparen = new Regex("(>|\\])", ")");\r
+//\r
+// // Detect if file is RNA by looking for bracket types\r
+// Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");\r
+//\r
+// rend.optimize();\r
+// p.optimize();\r
+// s.optimize();\r
+// r.optimize();\r
+// x.optimize();\r
+// openparen.optimize();\r
+// closeparen.optimize();\r
+//\r
+// while ((line = nextLine()) != null)\r
+// {\r
+// if (line.length() == 0)\r
+// {\r
+// continue;\r
+// }\r
+// if (rend.search(line))\r
+// {\r
+// // End of the alignment, pass stuff back\r
+//\r
+// this.noSeqs = seqs.size();\r
+// // logger.debug("Number of sequences: " + this.noSeqs);\r
+// Enumeration accs = seqs.keys();\r
+// while (accs.hasMoreElements())\r
+// {\r
+// String acc = (String) accs.nextElement();\r
+// // logger.debug("Processing sequence " + acc);\r
+// String seq = (String) seqs.remove(acc);\r
+// if (maxLength < seq.length())\r
+// {\r
+// maxLength = seq.length();\r
+// }\r
+// int start = 1;\r
+// int end = -1;\r
+// String sid = acc;\r
+// /*\r
+// * Retrieve hash of annotations for this accession\r
+// * Associate Annotation with accession\r
+// */\r
+// Hashtable accAnnotations = null;\r
+//\r
+// if (seqAnn != null && seqAnn.containsKey(acc))\r
+// {\r
+// accAnnotations = (Hashtable) seqAnn.remove(acc);\r
+// //TODO: add structures to sequence\r
+// }\r
+//\r
+// // Split accession in id and from/to\r
+// if (p.search(acc))\r
+// {\r
+// sid = p.stringMatched(1);\r
+// start = Integer.parseInt(p.stringMatched(2));\r
+// end = Integer.parseInt(p.stringMatched(3));\r
+// }\r
+// // logger.debug(sid + ", " + start + ", " + end);\r
+//\r
+// Sequence seqO = new Sequence(sid, seq, start, end);\r
+// // Add Description (if any)\r
+// if (accAnnotations != null && accAnnotations.containsKey("DE"))\r
+// {\r
+// String desc = (String) accAnnotations.get("DE");\r
+// seqO.setDescription((desc == null) ? "" : desc);\r
+// }\r
+// // Add DB References (if any)\r
+// if (accAnnotations != null && accAnnotations.containsKey("DR"))\r
+// {\r
+// String dbr = (String) accAnnotations.get("DR");\r
+// if (dbr != null && dbr.indexOf(";") > -1)\r
+// {\r
+// String src = dbr.substring(0, dbr.indexOf(";"));\r
+// String acn = dbr.substring(dbr.indexOf(";") + 1);\r
+// jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);\r
+// // seqO.addDBRef(dbref);\r
+// }\r
+// } \r
+// if (accAnnotations != null && accAnnotations.containsKey("SS"))\r
+// {\r
+// Vector v = (Vector) accAnnotations.get("SS");\r
+// \r
+// for (int i = 0; i < v.size(); i++)\r
+// {\r
+// AlignmentAnnotation an = (AlignmentAnnotation) v.elementAt(i);\r
+// seqO.addAlignmentAnnotation(an);\r
+// //annotations.add(an);\r
+// }\r
+// }\r
+// \r
+// Hashtable features = null;\r
+// // We need to adjust the positions of all features to account for gaps\r
+// try\r
+// {\r
+// features = (Hashtable) accAnnotations.remove("features");\r
+// } catch (java.lang.NullPointerException e)\r
+// {\r
+// // loggerwarn("Getting Features for " + acc + ": " +\r
+// // e.getMessage());\r
+// // continue;\r
+// }\r
+// // if we have features\r
+// if (features != null)\r
+// {\r
+// int posmap[] = seqO.findPositionMap();\r
+// Enumeration i = features.keys();\r
+// while (i.hasMoreElements())\r
+// {\r
+// // TODO: parse out secondary structure annotation as annotation\r
+// // row\r
+// // TODO: parse out scores as annotation row\r
+// // TODO: map coding region to core jalview feature types\r
+// String type = i.nextElement().toString();\r
+// Hashtable content = (Hashtable) features.remove(type);\r
+// Enumeration j = content.keys();\r
+// while (j.hasMoreElements())\r
+// {\r
+// String desc = j.nextElement().toString();\r
+// String ns = content.get(desc).toString();\r
+// char[] byChar = ns.toCharArray();\r
+// for (int k = 0; k < byChar.length; k++)\r
+// {\r
+// char c = byChar[k];\r
+// if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM\r
+// // uses\r
+// // '.'\r
+// // for\r
+// // feature\r
+// // background\r
+// {\r
+// int new_pos = posmap[k]; // look up nearest seqeunce\r
+// // position to this column\r
+// SequenceFeature feat = new SequenceFeature(type, desc,\r
+// new_pos, new_pos, 0f, null);\r
+//\r
+// seqO.addSequenceFeature(feat);\r
+// }\r
+// }\r
+// }\r
+//\r
+// }\r
+//\r
+// }\r
+// // garbage collect\r
+//\r
+// // logger.debug("Adding seq " + acc + " from " + start + " to " + end\r
+// // + ": " + seq);\r
+// this.seqs.addElement(seqO);\r
+// }\r
+// return; // finished parsing this segment of source\r
+// }\r
+// else if (!r.search(line))\r
+// {\r
+// // System.err.println("Found sequence line: " + line);\r
+//\r
+// // Split sequence in sequence and accession parts\r
+// if (!x.search(line))\r
+// {\r
+// // logger.error("Could not parse sequence line: " + line);\r
+// throw new IOException("Could not parse sequence line: " + line);\r
+// }\r
+// String ns = (String) seqs.get(x.stringMatched(1));\r
+// if (ns == null)\r
+// {\r
+// ns = "";\r
+// }\r
+// ns += x.stringMatched(2);\r
+//\r
+// seqs.put(x.stringMatched(1), ns);\r
+// }\r
+// else\r
+// {\r
+// String annType = r.stringMatched(1);\r
+// String annContent = r.stringMatched(2);\r
+//\r
+// // System.err.println("type:" + annType + " content: " + annContent);\r
+//\r
+// if (annType.equals("GF"))\r
+// {\r
+// /*\r
+// * Generic per-File annotation, free text Magic features: #=GF NH\r
+// * <tree in New Hampshire eXtended format> #=GF TN <Unique identifier\r
+// * for the next tree> Pfam descriptions: 7. DESCRIPTION OF FIELDS\r
+// * \r
+// * Compulsory fields: ------------------\r
+// * \r
+// * AC Accession number: Accession number in form PFxxxxx.version or\r
+// * PBxxxxxx. ID Identification: One word name for family. DE\r
+// * Definition: Short description of family. AU Author: Authors of the\r
+// * entry. SE Source of seed: The source suggesting the seed members\r
+// * belong to one family. GA Gathering method: Search threshold to\r
+// * build the full alignment. TC Trusted Cutoff: Lowest sequence score\r
+// * and domain score of match in the full alignment. NC Noise Cutoff:\r
+// * Highest sequence score and domain score of match not in full\r
+// * alignment. TP Type: Type of family -- presently Family, Domain,\r
+// * Motif or Repeat. SQ Sequence: Number of sequences in alignment. AM\r
+// * Alignment Method The order ls and fs hits are aligned to the model\r
+// * to build the full align. // End of alignment.\r
+// * \r
+// * Optional fields: ----------------\r
+// * \r
+// * DC Database Comment: Comment about database reference. DR Database\r
+// * Reference: Reference to external database. RC Reference Comment:\r
+// * Comment about literature reference. RN Reference Number: Reference\r
+// * Number. RM Reference Medline: Eight digit medline UI number. RT\r
+// * Reference Title: Reference Title. RA Reference Author: Reference\r
+// * Author RL Reference Location: Journal location. PI Previous\r
+// * identifier: Record of all previous ID lines. KW Keywords: Keywords.\r
+// * CC Comment: Comments. NE Pfam accession: Indicates a nested domain.\r
+// * NL Location: Location of nested domains - sequence ID, start and\r
+// * end of insert.\r
+// * \r
+// * Obsolete fields: ----------- AL Alignment method of seed: The\r
+// * method used to align the seed members.\r
+// */\r
+// // Let's save the annotations, maybe we'll be able to do something\r
+// // with them later...\r
+// Regex an = new Regex("(\\w+)\\s*(.*)");\r
+// if (an.search(annContent))\r
+// {\r
+// if (an.stringMatched(1).equals("NH"))\r
+// {\r
+// treeString.append(an.stringMatched(2));\r
+// }\r
+// else if (an.stringMatched(1).equals("TN"))\r
+// {\r
+// if (treeString.length() > 0)\r
+// {\r
+// if (treeName == null)\r
+// {\r
+// treeName = "Tree " + (getTreeCount() + 1);\r
+// }\r
+// addNewickTree(treeName, treeString.toString());\r
+// }\r
+// treeName = an.stringMatched(2);\r
+// treeString = new StringBuffer();\r
+// }\r
+// setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));\r
+// }\r
+// }\r
+// else if (annType.equals("GS"))\r
+// {\r
+// // Generic per-Sequence annotation, free text\r
+// /*\r
+// * Pfam uses these features: Feature Description ---------------------\r
+// * ----------- AC <accession> ACcession number DE <freetext>\r
+// * DEscription DR <db>; <accession>; Database Reference OS <organism>\r
+// * OrganiSm (species) OC <clade> Organism Classification (clade, etc.)\r
+// * LO <look> Look (Color, etc.)\r
+// */\r
+// if (s.search(annContent))\r
+// {\r
+// String acc = s.stringMatched(1);\r
+// String type = s.stringMatched(2);\r
+// String content = s.stringMatched(3);\r
+// // TODO: store DR in a vector.\r
+// // TODO: store AC according to generic file db annotation.\r
+// Hashtable ann;\r
+// if (seqAnn.containsKey(acc))\r
+// {\r
+// ann = (Hashtable) seqAnn.get(acc);\r
+// }\r
+// else\r
+// {\r
+// ann = new Hashtable();\r
+// }\r
+// ann.put(type, content);\r
+// seqAnn.put(acc, ann);\r
+// }\r
+// else\r
+// {\r
+// throw new IOException("Error parsing " + line);\r
+// }\r
+// }\r
+// else if (annType.equals("GC"))\r
+// {\r
+// // Generic per-Column annotation, exactly 1 char per column\r
+// // always need a label.\r
+// if (x.search(annContent))\r
+// {\r
+// // parse out and create alignment annotation directly.\r
+// parseAnnotationRow(annotations, x.stringMatched(1),\r
+// x.stringMatched(2));\r
+// }\r
+// }\r
+// else if (annType.equals("GR"))\r
+// {\r
+// // Generic per-Sequence AND per-Column markup, exactly 1 char per\r
+// // column\r
+// /*\r
+// * Feature Description Markup letters ------- -----------\r
+// * -------------- SS Secondary Structure [HGIEBTSCX] SA Surface\r
+// * Accessibility [0-9X] (0=0%-10%; ...; 9=90%-100%) TM TransMembrane\r
+// * [Mio] PP Posterior Probability [0-9*] (0=0.00-0.05; 1=0.05-0.15;\r
+// * *=0.95-1.00) LI LIgand binding [*] AS Active Site [*] IN INtron (in\r
+// * or after) [0-2]\r
+// */\r
+// if (s.search(annContent))\r
+// {\r
+// String acc = s.stringMatched(1);\r
+// String type = s.stringMatched(2);\r
+// String seq = new String(s.stringMatched(3));\r
+// String description = null;\r
+// // Check for additional information about the current annotation\r
+// // We use a simple string tokenizer here for speed\r
+// StringTokenizer sep = new StringTokenizer(seq, " \t");\r
+// description = sep.nextToken();\r
+// if (sep.hasMoreTokens())\r
+// {\r
+// seq = sep.nextToken();\r
+// }\r
+// else\r
+// {\r
+// seq = description;\r
+// description = new String();\r
+// }\r
+// // sequence id with from-to fields\r
+//\r
+// Hashtable ann;\r
+// // Get an object with all the annotations for this sequence\r
+// if (seqAnn.containsKey(acc))\r
+// {\r
+// // logger.debug("Found annotations for " + acc);\r
+// ann = (Hashtable) seqAnn.get(acc);\r
+// }\r
+// else\r
+// {\r
+// // logger.debug("Creating new annotations holder for " + acc);\r
+// ann = new Hashtable();\r
+// seqAnn.put(acc, ann);\r
+// }\r
+// //TODO test structure, call parseAnnotationRow with vector from hashtable for specific sequence\r
+// Hashtable features;\r
+// // Get an object with all the content for an annotation\r
+// if (ann.containsKey("features"))\r
+// {\r
+// // logger.debug("Found features for " + acc);\r
+// features = (Hashtable) ann.get("features");\r
+// }\r
+// else\r
+// {\r
+// // logger.debug("Creating new features holder for " + acc);\r
+// features = new Hashtable();\r
+// ann.put("features", features);\r
+// }\r
+//\r
+// Hashtable content;\r
+// if (features.containsKey(this.id2type(type)))\r
+// {\r
+// // logger.debug("Found content for " + this.id2type(type));\r
+// content = (Hashtable) features.get(this.id2type(type));\r
+// }\r
+// else\r
+// {\r
+// // logger.debug("Creating new content holder for " +\r
+// // this.id2type(type));\r
+// content = new Hashtable();\r
+// features.put(this.id2type(type), content);\r
+// }\r
+// String ns = (String) content.get(description);\r
+// if (ns == null)\r
+// {\r
+// ns = "";\r
+// }\r
+// ns += seq;\r
+// content.put(description, ns);\r
+//
+// if(type.equals("SS")){\r
+// Hashtable strucAnn;\r
+// if (seqAnn.containsKey(acc))\r
+// {\r
+// strucAnn = (Hashtable) seqAnn.get(acc);\r
+// }\r
+// else\r
+// {\r
+// strucAnn = new Hashtable();\r
+// }\r
+// \r
+// Vector newStruc=new Vector();\r
+// parseAnnotationRow(newStruc, type,ns);\r
+// \r
+// strucAnn.put(type, newStruc);\r
+// seqAnn.put(acc, strucAnn);\r
+// }\r
+// }\r
+// else\r
+// {\r
+// System.err\r
+// .println("Warning - couldn't parse sequence annotation row line:\n"\r
+// + line);\r
+// // throw new IOException("Error parsing " + line);\r
+// }\r
+// }\r
+// else\r
+// {\r
+// throw new IOException("Unknown annotation detected: " + annType\r
+// + " " + annContent);\r
+// }\r
+// }\r
+// }\r
+// if (treeString.length() > 0)\r
+// {\r
+// if (treeName == null)\r
+// {\r
+// treeName = "Tree " + (1 + getTreeCount());\r
+// }\r
+// addNewickTree(treeName, treeString.toString());\r
+// }\r
+// }\r
+//\r
protected static AlignmentAnnotation parseAnnotationRow(Vector annotation,\r
String label, String annots)\r
{\r
Regex openparen = new Regex("(<|\\[)", "(");\r
Regex closeparen = new Regex("(>|\\])", ")");\r
\r
- // Detect if file is RNA by looking for bracket types\r
+ // Detect if file is RNA by looking for bracket types\r
Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");\r
\r
convert1 = openparen.replaceAll(annots);\r
if (detectbrackets.search(pos))\r
{\r
ann.secondaryStructure = jalview.schemes.ResidueProperties\r
- .getRNASecStrucState(pos).charAt(0);\r
+ .getRNASecStrucState(pos).charAt(0);\r
}\r
else\r
{\r
ann.displayCharacter = ""; // null; // " ";\r
}\r
else\r
- {\r
+ {\r
ann.displayCharacter = " " + ann.displayCharacter;\r
}\r
}\r
\r
els[i] = ann;\r
}\r
- AlignmentAnnotation annot = null;\r
+ AlignmentAnnotation annot = null;\r
Enumeration e = annotation.elements();\r
while (e.hasMoreElements())\r
{\r
annotation.addElement(annot);\r
}\r
else\r
- {\r
+ {\r
Annotation[] anns = new Annotation[annot.annotations.length\r
+ els.length];\r
- System.arraycopy(annot.annotations, 0, anns, 0,\r
- annot.annotations.length);\r
+ System.arraycopy(annot.annotations, 0, anns, 0,\r
+ annot.annotations.length);\r
System.arraycopy(els, 0, anns, annot.annotations.length, els.length);\r
annot.annotations = anns;\r
//System.out.println("else: ");\r
- }\r
- return annot;\r
+ }\r
+ return annot;\r
}\r
\r
public static String print(SequenceI[] s)\r
* \r
* \r
* return helicesAnnot; }\r
+ * \r
*/\r
+ /**\r
+ * make a friendly ID string.\r
+ * \r
+ * @param dataName\r
+ * @return truncated dataName to after last '/'\r
+ */\r
+ private String safeName(String dataName)\r
+ {\r
+ int b = 0;\r
+ while ((b = dataName.indexOf("/")) > -1 && b < dataName.length() )\r
+ { \r
+ dataName = dataName.substring(b + 1).trim();\r
+ \r
+ }\r
+ int e = (dataName.length() - dataName.indexOf("."))+1;\r
+ dataName = dataName.substring(1,e).trim();\r
+ return dataName;\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff