import jalview.datamodel.SequenceFeature;\r
import jalview.datamodel.SequenceI;\r
\r
-import java.io.*;\r
-import java.util.*;\r
-\r
-\r
-import javax.xml.parsers.ParserConfigurationException;\r
-\r
-import org.xml.sax.SAXException;\r
+import java.io.BufferedReader;\r
+import java.io.FileReader;\r
+import java.io.IOException;\r
+import java.util.ArrayList;\r
+import java.util.Enumeration;\r
+import java.util.Hashtable;\r
+import java.util.StringTokenizer;\r
+import java.util.Vector;\r
\r
import com.stevesoft.pat.Regex;\r
\r
-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
\r
-\r
-\r
// import org.apache.log4j.*;\r
\r
/**\r
{\r
// static Logger logger = Logger.getLogger("jalview.io.StockholmFile");\r
protected ArrayList<RNA> result;\r
+\r
public String id;\r
- \r
+\r
public StockholmFile()\r
{\r
}\r
\r
- public StockholmFile(String inFile, String type) throws Exception \r
+ public StockholmFile(String inFile, String type) throws IOException\r
{\r
super(inFile, type);\r
}\r
\r
- public StockholmFile(FileParse source) throws Exception \r
+ public StockholmFile(FileParse source) throws IOException\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
{\r
- \r
StringBuffer treeString = new StringBuffer();\r
String treeName = null;\r
// --------------- Variable Definitions -------------------\r
}\r
}\r
\r
- protected static AlignmentAnnotation parseAnnotationRow(Vector annotation,\r
- String label, String annots)\r
+\r
+ /**\r
+ * Parse a file in Stockholm format into Jalview's data model using VARNA\r
+ * \r
+ * @throws IOException\r
+ * If there is an error with the input file\r
+ */\r
+ public void parse_with_VARNA() throws IOException\r
+ {\r
+ FileReader fr = null;\r
+ fr = new FileReader(inFile);\r
+\r
+ BufferedReader r = new BufferedReader(fr);\r
+ result = null;\r
+ try\r
+ {\r
+ result = RNAFactory.loadSecStrStockholm(r);\r
+ } catch (ExceptionUnmatchedClosingParentheses umcp)\r
+ {\r
+ errormessage = "Unmatched parentheses in annotation. Aborting ("\r
+ + umcp.getMessage() + ")";\r
+ throw new IOException(umcp);\r
+ }\r
+ // DEBUG System.out.println("this is the secondary scructure:"\r
+ // +result.size());\r
+ SequenceI[] seqs = new SequenceI[result.size()];\r
+ for (int i = 0; i < result.size(); i++)\r
+ {\r
+ // DEBUG System.err.println("Processing i'th sequence in Stockholm file")\r
+ RNA current = result.get(i);\r
+\r
+ String seq = current.getSeq();\r
+ String rna = current.getStructDBN(true);\r
+ // DEBUG System.out.println(seq);\r
+ // DEBUG System.err.println(rna);\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], "",\r
+ jalview.schemes.ResidueProperties.getRNASecStrucState(\r
+ annot[k]).charAt(0), 0f);\r
+\r
+ }\r
+ AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",\r
+ 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
+ protected static AlignmentAnnotation parseAnnotationRow(\r
+ Vector annotation, String label, String annots)\r
{\r
String convert1, convert2 = null;\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
+ // System.out.println("else: ");\r
+ }\r
+ return annot;\r
}\r
\r
public static String print(SequenceI[] s)\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
- /**\r
* make a friendly ID string.\r
* \r
* @param dataName\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
+ 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
+ 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