/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
* \r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
+ * This file is part of Jalview.\r
* \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
* \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
/*\r
* This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk\r
\r
import com.stevesoft.pat.*;\r
import jalview.datamodel.*;\r
+import jalview.analysis.Rna;\r
\r
// import org.apache.log4j.*;\r
\r
* be passed at construction time\r
* \r
* @throws IOException\r
- * If there is an error with the input file\r
+ * If there is an error with the input file\r
*/\r
public void parse() throws IOException\r
{\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
\r
// We define some Regexes here that will be used regularily later\r
- rend = new Regex("\\/\\/"); // Find the end of an alignment\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
int start = 1;\r
int end = -1;\r
String sid = acc;\r
- // Retrieve hash of annotations for this accession\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
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
char c = byChar[k];\r
if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM\r
- // uses\r
- // '.'\r
- // for\r
- // feature\r
- // background\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
+ // position to this column\r
SequenceFeature feat = new SequenceFeature(type, desc,\r
new_pos, new_pos, 0f, null);\r
\r
if (x.search(annContent))\r
{\r
// parse out and create alignment annotation directly.\r
- parseAnnotationRow(annotations, x.stringMatched(1), x\r
- .stringMatched(2));\r
+ parseAnnotationRow(annotations, x.stringMatched(1),\r
+ x.stringMatched(2));\r
}\r
}\r
else if (annType.equals("GR"))\r
ann = new Hashtable();\r
seqAnn.put(acc, ann);\r
}\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
ns = "";\r
}\r
ns += seq;\r
- content.put(description, 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
private AlignmentAnnotation parseAnnotationRow(Vector annotation,\r
String label, String annots)\r
{\r
+ String convert1, convert2 = null;\r
+\r
+ // Convert all bracket types to parentheses\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
+ convert1 = openparen.replaceAll(annots);\r
+ convert2 = closeparen.replaceAll(convert1);\r
+ annots = convert2;\r
+\r
String type = (label.indexOf("_cons") == label.length() - 5) ? label\r
.substring(0, label.length() - 5) : label;\r
boolean ss = false;\r
String pos = annots.substring(i, i + 1);\r
Annotation ann;\r
ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not\r
- // be written out\r
+ // be written out\r
if (ss)\r
{\r
- ann.secondaryStructure = jalview.schemes.ResidueProperties\r
- .getDssp3state(pos).charAt(0);\r
+ if (detectbrackets.search(pos))\r
+ {\r
+ ann.secondaryStructure = jalview.schemes.ResidueProperties\r
+ .getRNASecStrucState(pos).charAt(0);\r
+ }\r
+ else\r
+ {\r
+ ann.secondaryStructure = jalview.schemes.ResidueProperties\r
+ .getDssp3state(pos).charAt(0);\r
+ }\r
+\r
if (ann.secondaryStructure == pos.charAt(0) || pos.charAt(0) == 'C')\r
{\r
ann.displayCharacter = ""; // null; // " ";\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
+ id);\r
return id;\r
}\r
+ /**\r
+ * //ssline is complete secondary structure line private AlignmentAnnotation\r
+ * addHelices(Vector annotation, String label, String ssline) {\r
+ * \r
+ * // decide on secondary structure or not. Annotation[] els = new\r
+ * Annotation[ssline.length()]; for (int i = 0; i < ssline.length(); i++) {\r
+ * String pos = ssline.substring(i, i + 1); Annotation ann; ann = new\r
+ * Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not\r
+ * \r
+ * ann.secondaryStructure =\r
+ * jalview.schemes.ResidueProperties.getRNAssState(pos).charAt(0);\r
+ * \r
+ * ann.displayCharacter = "x" + ann.displayCharacter;\r
+ * \r
+ * System.out.println(ann.displayCharacter);\r
+ * \r
+ * els[i] = ann; } AlignmentAnnotation helicesAnnot = null; Enumeration e =\r
+ * annotation.elements(); while (e.hasMoreElements()) { helicesAnnot =\r
+ * (AlignmentAnnotation) e.nextElement(); if (helicesAnnot.label.equals(type))\r
+ * break; helicesAnnot = null; } if (helicesAnnot == null) { helicesAnnot =\r
+ * new AlignmentAnnotation(type, type, els);\r
+ * annotation.addElement(helicesAnnot); } else { Annotation[] anns = new\r
+ * Annotation[helicesAnnot.annotations.length + els.length];\r
+ * System.arraycopy(helicesAnnot.annotations, 0, anns, 0,\r
+ * helicesAnnot.annotations.length); System.arraycopy(els, 0, anns,\r
+ * helicesAnnot.annotations.length, els.length); helicesAnnot.annotations =\r
+ * anns; }\r
+ * \r
+ * helicesAnnot.features = Rna.GetBasePairs(ssline);\r
+ * Rna.HelixMap(helicesAnnot.features);\r
+ * \r
+ * \r
+ * return helicesAnnot; }\r
+ */\r
}\r
git://source.jalview.org / jalview.git / blobdiff