+++ /dev/null
-package fr.orsay.lri.varna.factories;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.Reader;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.EmptyStackException;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Stack;
-import java.util.Vector;
-
-import javax.xml.parsers.SAXParser;
-import javax.xml.parsers.SAXParserFactory;
-
-import org.xml.sax.InputSource;
-
-import fr.orsay.lri.varna.exceptions.ExceptionExportFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
-import fr.orsay.lri.varna.models.rna.ModeleBP;
-import fr.orsay.lri.varna.models.rna.ModeleBackboneElement;
-import fr.orsay.lri.varna.models.rna.ModeleBackboneElement.BackboneType;
-import fr.orsay.lri.varna.models.rna.ModeleBase;
-import fr.orsay.lri.varna.models.rna.RNA;
-import fr.orsay.lri.varna.utils.RNAMLParser;
-
-/**
- * BH JAVA FIX: mostly here we are just removing a lot of unnecessary stack traces when doing a drag-drop of a file
- * BH JAVA FIX: making sure the file reader is closed properly
- *
- */
-public class RNAFactory
-{
-
- public enum RNAFileType
- {
- FILE_TYPE_STOCKHOLM, FILE_TYPE_TCOFFEE, FILE_TYPE_BPSEQ, FILE_TYPE_CT, FILE_TYPE_DBN, FILE_TYPE_RNAML, FILE_TYPE_UNKNOWN
- }
-
-private static boolean isQuiet;
-
- public static ArrayList<RNA> loadSecStrRNAML(Reader r)
- throws ExceptionPermissionDenied, ExceptionLoadingFailed,
- ExceptionFileFormatOrSyntax
- {
-
- ArrayList<RNA> result = new ArrayList<RNA>();
- try
- {
- // System.setProperty("javax.xml.parsers.SAXParserFactory",
- // "com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl");
- SAXParserFactory saxFact = javax.xml.parsers.SAXParserFactory
- .newInstance();
- saxFact.setValidating(false);
- saxFact.setXIncludeAware(false);
- saxFact.setNamespaceAware(false);
- SAXParser sp = saxFact.newSAXParser();
- RNAMLParser RNAMLData = new RNAMLParser();
- sp.parse(new InputSource(r), RNAMLData);
-
- /*
- * XMLReader xr = XMLReaderFactory.createXMLReader(); RNAMLParser
- * RNAMLData = new RNAMLParser(); xr.setContentHandler(RNAMLData);
- * xr.setErrorHandler(RNAMLData); xr.setEntityResolver(RNAMLData);
- * xr.parse(new InputSource(r));
- */
- for (RNAMLParser.RNATmp rnaTmp : RNAMLData.getMolecules())
- {
- RNA current = new RNA();
- // Retrieving parsed data
- List<String> seq = rnaTmp.getSequence();
- // Creating empty structure of suitable size
- int[] str = new int[seq.size()];
- for (int i = 0; i < str.length; i++)
- {
- str[i] = -1;
- }
- current.setRNA(seq, str);
- Vector<RNAMLParser.BPTemp> allbpsTmp = rnaTmp.getStructure();
- ArrayList<ModeleBP> allbps = new ArrayList<ModeleBP>();
- for (int i = 0; i < allbpsTmp.size(); i++)
- {
- RNAMLParser.BPTemp bp = allbpsTmp.get(i);
- // System.err.println(bp);
- int bp5 = bp.pos5;
- int bp3 = bp.pos3;
- ModeleBase mb = current.getBaseAt(bp5);
- ModeleBase part = current.getBaseAt(bp3);
- ModeleBP newStyle = bp.createBPStyle(mb, part);
- allbps.add(newStyle);
- }
-
- current.applyBPs(allbps);
- result.add(current);
- }
-
- }
- catch (IOException ioe)
- {
- throw new ExceptionLoadingFailed(
- "Couldn't load file due to I/O or security policy issues.", "");
- }
- catch (Exception ge)
- {
- if (!isQuiet) // BH
- ge.printStackTrace();
- }
- return result;
- }
-
- public static int[] parseSecStr(String _secStr)
- throws ExceptionUnmatchedClosingParentheses
- {
- Hashtable<Character, Stack<Integer>> stacks = new Hashtable<Character, Stack<Integer>>();
- int[] result = new int[_secStr.length()];
- int i = 0;
- try
- {
- for (i = 0; i < _secStr.length(); i++)
- {
- result[i] = -1;
- char c = _secStr.charAt(i);
- char c2 = Character.toUpperCase(c);
- if (!stacks.containsKey(c2))
- {
- stacks.put(c2, new Stack<Integer>());
- }
- switch (c)
- {
- case '<':
- case '{':
- case '(':
- case '[':
- stacks.get(c).push(i);
- break;
- case '>':
- {
- int j = stacks.get('<').pop();
- result[i] = j;
- result[j] = i;
- break;
- }
- case '}':
- {
- int j = stacks.get('{').pop();
- result[i] = j;
- result[j] = i;
- break;
- }
- case ')':
- {
- int j = stacks.get('(').pop();
- result[i] = j;
- result[j] = i;
- break;
- }
- case ']':
- {
- int j = stacks.get('[').pop();
- result[i] = j;
- result[j] = i;
- break;
- }
- case '.':
- break;
- default:
- {
- if (Character.isLetter(c) && Character.isUpperCase(c))
- {
- stacks.get(c).push(i);
- }
- else if (Character.isLetter(c) && Character.isLowerCase(c))
- {
- int j = stacks.get(Character.toUpperCase(c)).pop();
- result[i] = j;
- result[j] = i;
- }
- }
- }
- }
- }
- catch (EmptyStackException e)
- {
- throw new ExceptionUnmatchedClosingParentheses(i);
- }
- return result;
- }
-
- public static ArrayList<RNA> loadSecStrDBN(Reader r)
- throws ExceptionLoadingFailed, ExceptionPermissionDenied,
- ExceptionUnmatchedClosingParentheses, ExceptionFileFormatOrSyntax
- {
- boolean loadOk = false;
- ArrayList<RNA> result = new ArrayList<RNA>();
- RNA current = new RNA();
- try
- {
- BufferedReader fr = new BufferedReader(r);
- String line = fr.readLine();
- String title = "";
- String seqTmp = "";
- String strTmp = "";
- while ((line != null) && (strTmp.equals("")))
- {
- line = line.trim();
- if (!line.startsWith(">"))
- {
- if (seqTmp.equals(""))
- {
- seqTmp = line;
- }
- else
- {
- strTmp = line;
- }
- }
- else
- {
- title = line.substring(1).trim();
- }
- line = fr.readLine();
- }
- if (strTmp.length() != 0)
- {
- current.setRNA(seqTmp, strTmp);
- current.setName(title);
- loadOk = true;
- }
- }
- catch (IOException e)
- {
- throw new ExceptionLoadingFailed(e.getMessage(), "");
- }
- if (loadOk)
- {
- result.add(current);
- }
- return result;
- }
-
- public static ArrayList<RNA> loadSecStr(File f)
- throws ExceptionFileFormatOrSyntax
- {
- try {
- return loadSecStr(new BufferedReader(new FileReader(f)), RNAFileType.FILE_TYPE_UNKNOWN);
- } catch (FileNotFoundException e) {
- throw new ExceptionFileFormatOrSyntax(f.toString());
- }
- }
-
- public static ArrayList<RNA> loadSecStr(Reader r)
- throws ExceptionFileFormatOrSyntax
- {
- return loadSecStr(new BufferedReader(r), RNAFileType.FILE_TYPE_UNKNOWN);
- }
-
- public static ArrayList<RNA> loadSecStr(BufferedReader r, RNAFileType fileType) throws ExceptionFileFormatOrSyntax {
- try {
- switch (fileType) {
- case FILE_TYPE_DBN: {
- try {
- ArrayList<RNA> result = loadSecStrDBN(r);
- if (result.size() != 0)
- return result;
- } catch (Exception e) {
- }
- }
- break;
- case FILE_TYPE_CT: {
- try {
- ArrayList<RNA> result = loadSecStrCT(r);
- if (result.size() != 0)
- return result;
- } catch (Exception e) {
- if (!isQuiet) // BH
- e.printStackTrace();
- }
- }
- break;
- case FILE_TYPE_BPSEQ: {
- try {
- ArrayList<RNA> result = loadSecStrBPSEQ(r);
- if (result.size() != 0)
- return result;
- } catch (Exception e) {
- if (!isQuiet) // BH
- e.printStackTrace();
- }
- }
- break;
- case FILE_TYPE_TCOFFEE: {
- try {
- ArrayList<RNA> result = loadSecStrTCoffee(r);
- if (result.size() != 0)
- return result;
- } catch (Exception e) {
- if (!isQuiet) // BH
- e.printStackTrace();
- }
- }
- break;
- case FILE_TYPE_STOCKHOLM: {
- try {
- ArrayList<RNA> result = loadSecStrStockholm(r);
- if (result.size() != 0)
- return result;
- } catch (Exception e) {
- if (!isQuiet) // BH
- e.printStackTrace();
- }
- }
- break;
- case FILE_TYPE_RNAML: {
- try {
- ArrayList<RNA> result = loadSecStrRNAML(r);
- if (result.size() != 0)
- return result;
- } catch (Exception e) {
- if (!isQuiet) // BH
- e.printStackTrace();
- }
- }
- break;
-
- case FILE_TYPE_UNKNOWN: {
- try {
- r.mark(1000000);
- RNAFactory.RNAFileType[] types = RNAFactory.RNAFileType.values();
- isQuiet = true; // BH to not report errors when
- // drag-dropping
- ArrayList<RNA> result = null;
- RNAFactory.RNAFileType t = null;
- for (int i = 0; i < types.length; i++) {
- r.reset();
- t = types[i];
- if (t != RNAFactory.RNAFileType.FILE_TYPE_UNKNOWN) {
- try {
- result = loadSecStr(r, t);
- if (result.size() != 0) {
- break;
- }
- } catch (Exception e) {
- if (!isQuiet) // BH
- System.err.println(e.toString());
- }
- }
- }
- System.out.println(t); // BH
- isQuiet = false; // BH
- return result;
- } catch (IOException e2) {
- e2.printStackTrace();
- }
- }
- }
- throw new ExceptionFileFormatOrSyntax("Couldn't parse this file as " + fileType + ".");
- } finally { // BH !!
- try {
- if (!isQuiet)
- r.close();
- } catch (IOException e) {
- // ignore
- }
- }
- }
-
- public static RNAFileType guessFileTypeFromExtension(String path)
- {
- if (path.toLowerCase().endsWith("ml"))
- {
- return RNAFileType.FILE_TYPE_RNAML;
- }
- else if (path.toLowerCase().endsWith("dbn")
- || path.toLowerCase().endsWith("faa"))
- {
- return RNAFileType.FILE_TYPE_DBN;
- }
- else if (path.toLowerCase().endsWith("ct"))
- {
- return RNAFileType.FILE_TYPE_CT;
- }
- else if (path.toLowerCase().endsWith("bpseq"))
- {
- return RNAFileType.FILE_TYPE_BPSEQ;
- }
- else if (path.toLowerCase().endsWith("rfold"))
- {
- return RNAFileType.FILE_TYPE_TCOFFEE;
- }
- else if (path.toLowerCase().endsWith("stockholm")
- || path.toLowerCase().endsWith("stk"))
- {
- return RNAFileType.FILE_TYPE_STOCKHOLM;
- }
-
- return RNAFileType.FILE_TYPE_UNKNOWN;
-
- }
-
- public static ArrayList<RNA> loadSecStr(String path)
- throws ExceptionExportFailed, ExceptionPermissionDenied,
- ExceptionLoadingFailed, ExceptionFileFormatOrSyntax,
- ExceptionUnmatchedClosingParentheses, FileNotFoundException
- {
- FileReader fr = null;
- try
- {
- fr = new FileReader(path);
- RNAFileType type = guessFileTypeFromExtension(path);
- return loadSecStr(new BufferedReader(fr), type);
- }
- catch (ExceptionFileFormatOrSyntax e)
- {
- if (fr != null)
- try
- {
- fr.close();
- }
- catch (IOException e2)
- {
- }
- e.setPath(path);
- throw e;
- }
- }
-
- public static ArrayList<RNA> loadSecStrStockholm(BufferedReader r)
- throws IOException, ExceptionUnmatchedClosingParentheses
- {
- RNAAlignment a = StockholmIO.readAlignement(r);
- return a.getRNAs();
- }
-
- public static ArrayList<RNA> loadSecStrBPSEQ(Reader r)
- throws ExceptionPermissionDenied, ExceptionLoadingFailed,
- ExceptionFileFormatOrSyntax
- {
- boolean loadOk = false;
- ArrayList<RNA> result = new ArrayList<RNA>();
- RNA current = new RNA();
- try
- {
- BufferedReader fr = new BufferedReader(r);
- String line = fr.readLine();
- ArrayList<String> seqTmp = new ArrayList<String>();
- Hashtable<Integer, Vector<Integer>> strTmp = new Hashtable<Integer, Vector<Integer>>();
-
- int bpFrom;
- String base;
- int bpTo;
- int minIndex = -1;
- boolean noWarningYet = true;
- String title = "";
- String id = "";
- String filenameStr = "Filename:";
- String organismStr = "Organism:";
- String ANStr = "Accession Number:";
- while (line != null)
- {
- line = line.trim();
- String[] tokens = line.split("\\s+");
- ArrayList<Integer> numbers = new ArrayList<Integer>();
- Hashtable<Integer,Integer> numberToIndex = new Hashtable<Integer,Integer>();
- if ((tokens.length >= 3) && !tokens[0].contains("#")
- && !line.startsWith("Organism:") && !line.startsWith("Citation")
- && !line.startsWith("Filename:")
- && !line.startsWith("Accession Number:"))
- {
- base = tokens[1];
- seqTmp.add(base);
- bpFrom = (Integer.parseInt(tokens[0]));
- numbers.add(bpFrom);
- if (minIndex < 0)
- minIndex = bpFrom;
-
- if (seqTmp.size() < (bpFrom - minIndex + 1))
- {
- if (noWarningYet)
- {
- noWarningYet = false;
- /*
- * warningEmition( "Discontinuity detected between nucleotides " +
- * (seqTmp.size()) + " and " + (bpFrom + 1) +
- * "!\nFilling in missing portions with unpaired unknown 'X' nucleotides ..."
- * );
- */
- }
- while (seqTmp.size() < (bpFrom - minIndex + 1))
- {
- // System.err.println(".");
- seqTmp.add("X");
- }
- }
- for (int i = 2; i < tokens.length; i++)
- {
- bpTo = (Integer.parseInt(tokens[i]));
- if ((bpTo != 0) || (i != tokens.length - 1))
- {
- if (!strTmp.containsKey(bpFrom))
- strTmp.put(bpFrom, new Vector<Integer>());
- strTmp.get(bpFrom).add(bpTo);
- }
- }
- }
- else if (tokens[0].startsWith("#"))
- {
- int occur = line.indexOf("#");
- String tmp = line.substring(occur + 1);
- title += tmp.trim() + " ";
- }
- else if (tokens[0].startsWith(filenameStr))
- {
- int occur = line.indexOf(filenameStr);
- String tmp = line.substring(occur + filenameStr.length());
- title += tmp.trim();
- }
- else if (tokens[0].startsWith(organismStr))
- {
- int occur = line.indexOf(organismStr);
- String tmp = line.substring(occur + organismStr.length());
- if (title.length() != 0)
- {
- title = "/" + title;
- }
- title = tmp.trim() + title;
- }
- else if (line.contains(ANStr))
- {
- int occur = line.indexOf(ANStr);
- String tmp = line.substring(occur + ANStr.length());
- id = tmp.trim();
- }
- line = fr.readLine();
- }
- if (strTmp.size() != 0)
- {
- ArrayList<String> seq = seqTmp;
- int[] str = new int[seq.size()];
- for (int i = 0; i < seq.size(); i++)
- {
- str[i] = -1;
- }
- current.setRNA(seq, str, minIndex);
- ArrayList<ModeleBP> allbps = new ArrayList<ModeleBP>();
- for (int i : strTmp.keySet())
- {
- for (int j : strTmp.get(i))
- {
- if (i<=j)
- {
- ModeleBase mb = current.getBaseAt(i - minIndex);
- ModeleBase part = current.getBaseAt(j - minIndex);
- ModeleBP newStyle = new ModeleBP(mb, part);
- allbps.add(newStyle);
- }
- }
- }
- current.applyBPs(allbps);
- current.setName(title);
- current.setID(id);
- loadOk = true;
- }
- }
- catch (NumberFormatException e)
- {
- if (!isQuiet) // BH SwingJS
- e.printStackTrace();
- }
- catch (IOException e)
- {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- catch (Exception e)
- {
- throw new ExceptionLoadingFailed(e.getMessage(), "");
- }
- if (loadOk)
- result.add(current);
- return result;
- }
-
- public static ArrayList<RNA> loadSecStrTCoffee(Reader r)
- throws ExceptionPermissionDenied, ExceptionLoadingFailed,
- ExceptionFileFormatOrSyntax
- {
- boolean loadOk = false;
- ArrayList<RNA> result = new ArrayList<RNA>();
- try
- {
- BufferedReader fr = new BufferedReader(r);
- String line = fr.readLine();
- ArrayList<String> seqs = new ArrayList<String>();
- ArrayList<String> ids = new ArrayList<String>();
- int numSeqs = -1;
- int currSeq = -1;
- RNA current = null;
- while (line != null)
- {
- if (!line.startsWith("!"))
- {
- String[] tokens = line.split("\\s+");
- // This may indicate new secondary structure
- if (line.startsWith("#"))
- {
- currSeq = Integer.parseInt(tokens[0].substring(1));
- int currSeq2 = Integer.parseInt(tokens[1]);
- // For TCoffee, a sec str is a matching between a seq and itself
- // => Disregard any alignment by filtering on the equality of sequence indices.
- if (currSeq == currSeq2)
- {
- current = new RNA();
- current.setName(ids.get(currSeq - 1));
- current.setSequence(seqs.get(currSeq - 1));
- result.add(current);
- }
- else
- {
- current = null;
- }
- }
- // Beginning of the file...
- else if (current == null)
- {
- //... either this is the number of sequences...
- if (numSeqs < 0)
- {
- numSeqs = Integer.parseInt(tokens[0]);
- }
- //... or this is a sequence definition...
- else
- {
- String id = tokens[0];
- String seq = tokens[2];
- seqs.add(seq);
- ids.add(id);
- }
- }
- //Otherwise, this is a base-pair definition, related to the currently selected sequence
- else if (tokens.length == 3)
- {
- int from = Integer.parseInt(tokens[0]) - 1;
- int to = Integer.parseInt(tokens[1]) - 1;
- current.addBP(from, to);
- }
- }
- line = fr.readLine();
- }
- loadOk = true;
- }
- catch (NumberFormatException e)
- {
- if (!isQuiet) // BH SwingJS
- e.printStackTrace();
- }
- catch (IOException e)
- {
- if (!isQuiet) // BH SwingJS
- e.printStackTrace();
- }
- if (!loadOk)
- {
- throw new ExceptionLoadingFailed("Parse Error", "");
- }
- return result;
- }
-
- public static ArrayList<RNA> loadSecStrCT(Reader r)
- throws ExceptionPermissionDenied, ExceptionLoadingFailed,
- ExceptionFileFormatOrSyntax
- {
- boolean loadOk = false;
- ArrayList<RNA> result = new ArrayList<RNA>();
- RNA current = new RNA();
- try
- {
- BufferedReader fr = new BufferedReader(r);
- String line = fr.readLine();
- ArrayList<String> seq = new ArrayList<String>();
- ArrayList<String> lbls = new ArrayList<String>();
- Vector<Integer> strTmp = new Vector<Integer>();
- Vector<Integer> newStrands = new Vector<Integer>();
- int bpFrom;
- String base;
- String lbl;
- int bpTo;
- boolean noWarningYet = true;
- int minIndex = -1;
- String title = "";
- while (line != null)
- {
- line = line.trim();
- String[] tokens = line.split("\\s+");
- if (tokens.length >= 6)
- {
- try
- {
- bpFrom = (Integer.parseInt(tokens[0]));
- bpTo = (Integer.parseInt(tokens[4]));
- if (minIndex == -1)
- minIndex = bpFrom;
- bpFrom -= minIndex;
- if (bpTo != 0)
- bpTo -= minIndex;
- else
- bpTo = -1;
- base = tokens[1];
- lbl = tokens[5];
- int before = Integer.parseInt(tokens[2]);
- int after = Integer.parseInt(tokens[3]);
-
- if (before==0 && !seq.isEmpty())
- {
- newStrands.add(strTmp.size()-1);
- }
- if (bpFrom != seq.size())
- {
- if (noWarningYet)
- {
- noWarningYet = false;
- /*
- * warningEmition( "Discontinuity detected between nucleotides "
- * + (seq.size()) + " and " + (bpFrom + 1) +
- * "!\nFilling in missing portions with unpaired unknown 'X' nucleotides ..."
- * );
- */
- }
- while (bpFrom > seq.size())
- {
- seq.add("X");
- strTmp.add(-1);
- lbls.add("");
- }
- }
- seq.add(base);
- strTmp.add(bpTo);
- lbls.add(lbl);
- }
- catch (NumberFormatException e)
- {
- if (strTmp.size()!=0)
- e.printStackTrace();
- }
- }
- if ((line.contains("ENERGY = ")) || line.contains("dG = "))
- {
- String[] ntokens = line.split("\\s+");
- if (ntokens.length >= 4)
- {
- String energy = ntokens[3];
- for (int i = 4; i < ntokens.length; i++)
- {
- title += ntokens[i] + " ";
- }
- title += "(E=" + energy + " kcal/mol)";
- }
- }
- line = fr.readLine();
- }
- if (strTmp.size() != 0)
- {
- int[] str = new int[strTmp.size()];
- for (int i = 0; i < strTmp.size(); i++)
- {
- str[i] = strTmp.elementAt(i).intValue();
- }
- current.setRNA(seq, str, minIndex);
- current.setName(title);
- for (int i = 0; i < current.getSize(); i++)
- {
- current.getBaseAt(i).setLabel(lbls.get(i));
- }
- for (int i : newStrands)
- {
- current.getBackbone().addElement(new ModeleBackboneElement(i,BackboneType.DISCONTINUOUS_TYPE));
- }
-
-
- loadOk = true;
- }
- }
- catch (IOException e)
- {
- e.printStackTrace();
- throw new ExceptionLoadingFailed(e.getMessage(), "");
- }
- catch (NumberFormatException e)
- {
- if (!isQuiet) // BH SwingJS
- e.printStackTrace();
- throw new ExceptionFileFormatOrSyntax(e.getMessage(), "");
- }
- if (loadOk)
- result.add(current);
- return result;
- }
-
-}
git://source.jalview.org / jalview.git / blobdiff