X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;fp=src%2Fjalview%2Fio%2FStockholmFile.java;h=92f73f4efa26680c09703bbd4bb9ba766b6a2e44;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=84e629e043e85055e787ef5d33bc6d4d90d81e58;hpb=d4ec118f86b5c9dee801e743c46aaacc7bb521d1;p=jalview.git diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index 84e629e..92f73f4 100644 --- a/src/jalview/io/StockholmFile.java +++ b/src/jalview/io/StockholmFile.java @@ -36,6 +36,7 @@ import jalview.schemes.ResidueProperties; import jalview.util.Comparison; import jalview.util.Format; import jalview.util.MessageManager; +import jalview.util.Platform; import java.io.BufferedReader; import java.io.FileReader; @@ -76,20 +77,105 @@ public class StockholmFile extends AlignFile { private static final String ANNOTATION = "annotation"; -// private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "("); -// -// private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")"); + // WUSS extended symbols. Avoid ambiguity with protein SS annotations by using + // NOT_RNASS first. - public static final Regex DETECT_BRACKETS = new Regex( - "(<|>|\\[|\\]|\\(|\\)|\\{|\\})"); - - // WUSS extended symbols. Avoid ambiguity with protein SS annotations by using NOT_RNASS first. public static final String RNASS_BRACKETS = "<>[](){}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz"; + public static final int REGEX_STOCKHOLM = 0; + + public static final int REGEX_BRACKETS = 1; + // use the following regex to decide an annotations (whole) line is NOT an RNA // SS (it contains only E,H,e,h and other non-brace/non-alpha chars) - private static final Regex NOT_RNASS = new Regex( - "^[^<>[\\](){}A-DF-Za-df-z]*$"); + public static final int REGEX_NOT_RNASS = 2; + + private static final int REGEX_ANNOTATION = 3; + + private static final int REGEX_PFAM = 4; + + private static final int REGEX_RFAM = 5; + + private static final int REGEX_ALIGN_END = 6; + + private static final int REGEX_SPLIT_ID = 7; + + private static final int REGEX_SUBTYPE = 8; + + private static final int REGEX_ANNOTATION_LINE = 9; + + private static final int REGEX_REMOVE_ID = 10; + + private static final int REGEX_OPEN_PAREN = 11; + + private static final int REGEX_CLOSE_PAREN = 12; + + public static final int REGEX_MAX = 13; + + private static Regex REGEX[] = new Regex[REGEX_MAX]; + + /** + * Centralize all actual Regex instantialization in Platform. + * + * @param id + * @return + */ + private static Regex getRegex(int id) + { + if (REGEX[id] == null) + { + String pat = null, pat2 = null; + switch (id) + { + case REGEX_STOCKHOLM: + pat = "# STOCKHOLM ([\\d\\.]+)"; + break; + case REGEX_BRACKETS: + // for reference; not used + pat = "(<|>|\\[|\\]|\\(|\\)|\\{|\\})"; + break; + case REGEX_NOT_RNASS: + pat = "^[^<>[\\](){}A-DF-Za-df-z]*$"; + break; + case REGEX_ANNOTATION: + pat = "(\\w+)\\s*(.*)"; + break; + case REGEX_PFAM: + pat = "PF[0-9]{5}(.*)"; + break; + case REGEX_RFAM: + pat = "RF[0-9]{5}(.*)"; + break; + case REGEX_ALIGN_END: + pat = "^\\s*\\/\\/"; + break; + case REGEX_SPLIT_ID: + pat = "(\\S+)\\/(\\d+)\\-(\\d+)"; + break; + case REGEX_SUBTYPE: + pat = "(\\S+)\\s+(\\S*)\\s+(.*)"; + break; + case REGEX_ANNOTATION_LINE: + pat = "#=(G[FSRC]?)\\s+(.*)"; + break; + case REGEX_REMOVE_ID: + pat = "(\\S+)\\s+(\\S+)"; + break; + case REGEX_OPEN_PAREN: + pat = "(<|\\[)"; + pat2 = "("; + break; + case REGEX_CLOSE_PAREN: + pat = "(>|\\])"; + pat2 = ")"; + break; + default: + return null; + } + REGEX[id] = Platform.newRegex(pat, pat2); + } + return REGEX[id]; + } StringBuffer out; // output buffer @@ -214,7 +300,7 @@ public class StockholmFile extends AlignFile // First, we have to check that this file has STOCKHOLM format, i.e. the // first line must match - r = new Regex("# STOCKHOLM ([\\d\\.]+)"); + r = getRegex(REGEX_STOCKHOLM); if (!r.search(nextLine())) { throw new IOException(MessageManager @@ -228,19 +314,22 @@ public class StockholmFile extends AlignFile } // We define some Regexes here that will be used regularily later - rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment - p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in + rend = getRegex(REGEX_ALIGN_END);//"^\\s*\\/\\/"); // Find the end of an alignment + p = getRegex(REGEX_SPLIT_ID);//"(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in // id/from/to - s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype - r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line - x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence + s = getRegex(REGEX_SUBTYPE);// "(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses + // annotation subtype + r = getRegex(REGEX_ANNOTATION_LINE);// "#=(G[FSRC]?)\\s+(.*)"); // Finds any + // annotation line + x = getRegex(REGEX_REMOVE_ID);// "(\\S+)\\s+(\\S+)"); // split id from + // sequence // Convert all bracket types to parentheses (necessary for passing to VARNA) - Regex openparen = new Regex("(<|\\[)", "("); - Regex closeparen = new Regex("(>|\\])", ")"); + Regex openparen = getRegex(REGEX_OPEN_PAREN);//"(<|\\[)", "("); + Regex closeparen = getRegex(REGEX_CLOSE_PAREN);//"(>|\\])", ")"); // // Detect if file is RNA by looking for bracket types -// Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))"); + // Regex detectbrackets = getRegex("(<|>|\\[|\\]|\\(|\\))"); rend.optimize(); p.optimize(); @@ -262,8 +351,8 @@ public class StockholmFile extends AlignFile this.noSeqs = seqs.size(); String dbsource = 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 + Regex pf = getRegex(REGEX_PFAM); // Finds AC for Pfam + Regex rf = getRegex(REGEX_RFAM); // Finds AC for Rfam if (getAlignmentProperty("AC") != null) { String dbType = getAlignmentProperty("AC").toString(); @@ -507,7 +596,7 @@ public class StockholmFile extends AlignFile */ // Let's save the annotations, maybe we'll be able to do something // with them later... - Regex an = new Regex("(\\w+)\\s*(.*)"); + Regex an = getRegex(REGEX_ANNOTATION); if (an.search(annContent)) { if (an.stringMatched(1).equals("NH")) @@ -837,7 +926,8 @@ public class StockholmFile extends AlignFile if (type.equalsIgnoreCase("secondary structure")) { ss = true; - isrnass = !NOT_RNASS.search(annots); // sorry about the double negative + isrnass = !getRegex(REGEX_NOT_RNASS).search(annots); // sorry about the double + // negative // here (it's easier for dealing with // other non-alpha-non-brace chars) } @@ -998,7 +1088,7 @@ public class StockholmFile extends AlignFile while (en.hasMoreElements()) { Object idd = en.nextElement(); - String type = (String) dataRef.remove(idd); + String type = dataRef.remove(idd); out.append(new Format("%-" + (maxid - 2) + "s") .form("#=GS " + idd.toString() + " ")); if (type.contains("PFAM") || type.contains("RFAM"))