-package compbio.data.sequence;
-
-import java.io.BufferedReader;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Scanner;
-import java.util.TreeSet;
-import java.util.regex.Pattern;
-
-import org.apache.log4j.Logger;
-
-import compbio.runner.structure.RNAalifold;
-
-// Utility class for reading alifold output
-
-public class RNAStructReader {
-
- private static Logger log = Logger.getLogger(RNAStructReader.class);
-
- // Whitespace patterns
- static String s = "[+\\s=]+";
- static String bracket = "\\(|\\)|\\{|\\}|\\[|\\]";
- static String notData = "[\\s=+]+";
-
- // RNAOut data type patterns
- static String seqP = "[_\\-a-zA-Z]{2,}"; // Has to match --mis output aswell (not just ACGU_)
- static String structP = "[\\.)({}\\[\\],]{2,}";
- static String floatP = "-?\\d+\\.\\d*(e[+\\-]\\d+)?";
- static String energyP = "-?[0-9]*\\.?[0-9]{2}";
- static String freqP = "^-?\\d\\.\\d{6,}(e[+\\-]\\d+)?$";
-
- // alifold out line patterns
- static String ps = "\\s*";
- static String alignmentP = "^"+seqP+ps+"$";
- static String stdStructP = "^"+structP+s+"\\("+ps+floatP+s+floatP+s+floatP+ps+"\\)"+ps+"$";
- static String justStructP = "^"+structP+ps+"$";
- static String stochBTStructP = "^"+structP+s+floatP+s+floatP+ps+"$";
- static String PStructP = "^"+structP+s+"\\["+ps+floatP+ps+"\\]"+ps+"$";
- static String centStructP = "^"+structP+s+floatP+ps+"\\{"+ps+floatP+s+floatP+ps+"\\}"+ps+"$";
- static String MEAStructP = "^"+structP+s+"\\{"+ps+floatP+s+"MEA="+floatP+ps+"\\}"+ps+"$";
- static String freeEnergyP = "^"+ps+"free energy of ensemble"+ps+"="+ps+floatP+ps+"kcal/mol"+ps+"$";
- static String ensembleFreqP = "^"+ps+"frequency of mfe structure in ensemble "+floatP+ps+"$";
-
- public static ScoreManager readRNAStructStream(InputStream stdout)
- throws IOException {
-
- String error = "Error in parsing alifold stdout file: ";
- // The Lists required to construct a ScoreManager Using the new constructor
- List<String> structs = new ArrayList<String>();
- List<TreeSet<Score>> data = new ArrayList<TreeSet<Score>>();
-
- // Allocate necessry data structures for creating Score objects
- ArrayList<Float> scores = new ArrayList<Float>();
-
- BufferedReader reader = new BufferedReader(new InputStreamReader(stdout));
- // The first 2 lines of the alifold stdout file are always the same format
- String fline = reader.readLine();
- assert (Pattern.matches(AlifoldLine.alignment.regex, fline)) :
- error + "Sequence Alignment Expected";
- structs.add(fline.trim());
- data.add(newEmptyScore(AlifoldResult.alifoldSeq));
-
- fline = reader.readLine();
- assert (Pattern.matches(AlifoldLine.stdStruct.regex, fline)) :
- error + "Consensus Structure and Energy Expected";
- Scanner sc = new Scanner(fline);
- structs.add(sc.next());
- for (int i = 0; i < 3; i++) {
- scores.add(Float.parseFloat(sc.findInLine(floatP)));
- }
- data.add(newSetScore(AlifoldResult.alifold, scores));
-
- // Now the alifold stdout file formats diverge based on arguments
- fline = reader.readLine();
- String sline;
- Scanner nsc = null;
- while ( fline != null) {
- scores.clear();
- AlifoldLine ftype = identifyLine(fline);
- sline = reader.readLine(); // Look ahead
- sc = new Scanner(fline);
- if (sline != null) nsc = new Scanner(sline);
-
- if (ftype.equals(AlifoldLine.PStruct)) {
- // The -p or --MEA option is specified
- // The next line should always be frequency of mfe structure
- assert ( sline != null && Pattern.matches(AlifoldLine.ensembleFreq.regex, sline)) :
- error + "Expected frequency of mfe structure";
- structs.add(sc.next());
- scores.add(Float.parseFloat(sc.findInLine(floatP)));
- scores.add(Float.parseFloat(nsc.findInLine(floatP)));
- data.add(newSetScore(AlifoldResult.alifoldP, scores));
- // Jump line
- sline = reader.readLine();
- }
- else if (ftype.equals(AlifoldLine.centStruct)) {
- structs.add(sc.next());
- for (int i = 0; i < 3; i++) {
- scores.add(Float.parseFloat(sc.findInLine(floatP)));
- }
- data.add(newSetScore(AlifoldResult.alifoldCentroid, scores));
- }
- else if (ftype.equals(AlifoldLine.MEAStruct)) {
- structs.add(sc.next());
- for (int i = 0; i < 2; i++) {
- scores.add(Float.parseFloat(sc.findInLine(floatP)));
- }
- data.add(newSetScore(AlifoldResult.alifoldMEA, scores));
- }
- else if (ftype.equals(AlifoldLine.justStruct)) {
- structs.add(sc.next());
- data.add(newEmptyScore(AlifoldResult.alifoldStochBT));
- }
- else if (ftype.equals(AlifoldLine.stochBTStruct)) {
- structs.add(sc.next());
- scores.add(sc.nextFloat());
- scores.add(sc.nextFloat());
- data.add(newSetScore(AlifoldResult.alifoldStochBT, scores));
- }
- else if (ftype.equals(AlifoldLine.freeEnergy)) {
- assert (sline != null
- && Pattern.matches(AlifoldLine.ensembleFreq.regex, sline)) :
- error + "Found 'freeEnergy' line on its own";
- structs.add("Free energy of ensemble (kcal/mol) followed by "
- + "frequency of mfe structure in ensemble");
- scores.add(Float.parseFloat(sc.findInLine(floatP)));
- scores.add(Float.parseFloat(nsc.findInLine(floatP)));
- data.add(newSetScore(AlifoldResult.alifoldMetadata, scores));
- // jump line
- sline = reader.readLine();
- }
-
-
- assert(!ftype.equals(AlifoldLine.ensembleFreq)) :
- error + "Wasn't expecting 'frequency of mfe structure'!";
- assert(!ftype.equals(AlifoldLine.stdStruct)) :
- error + "'Standard output' line at a place other than line 2!";
- assert(!ftype.equals(AlifoldLine.alignment)) :
- error + "Wasn't expecting an alignment sequence!";
- assert(!ftype.equals(AlifoldLine.OTHER)) :
- error + "Wasn't expecting this whatever it is: " + fline;
- if (Pattern.matches("^\\s*$", fline)) {
- log.warn("While parsing alifold stdout: A line is either empty or"
- + " contains only whitespace");
- }
-
- fline = sline;
- }
-
- sc.close();
- if (nsc != null) nsc.close();
-
- return new ScoreManager(new RNAStruct(structs, data));
- }
-
- // Just for the purpose of creating nee TreeSet<Score> objects of length one
- // for adding to a 'data' list to make a ScoreManager
- private static TreeSet<Score> newSetScore(Enum<?> res, List<Float> scores) {
- // first convert List<Float> to float[]
- float[] scoresf = new float[scores.size()];
- Float f;
- for (int i = 0; i < scoresf.length; i++) {
- f = scores.get(i);
- scoresf[i] = ( f != null ? f : Float.NaN);
- }
- return new TreeSet<Score>(Arrays.asList(new Score(res, scoresf)));
- }
-
- // A method just for the purpose of neatly creating Almost Empty score objects
- // that can't be null
- public static TreeSet<Score> newEmptyScore(Enum<?> res) {
- return new TreeSet<Score>(Arrays.asList(new Score(res, new float[0])));
- }
-
- public static ScoreManager readRNAStructStream(InputStream stdout,
- InputStream alifold) throws IOException {
-
- // The Lists required to construct a ScoreManager Using the new constructor
- List<String> structs;
- List<TreeSet<Score>> data;
-
- // Get a ScoreManager that takes the std output but ignores alifold.out (-p)
- ScoreManager stdSM = readRNAStructStream(stdout);
-
- // Unpack this into the structs and data lists
- structs = stdSM.asRNAStruct().getStructs();
- data = stdSM.asRNAStruct().getData();
-
- // Now parse alifold.out
- Scanner sc = new Scanner(alifold);
- sc.useDelimiter("[\\s%]+");
-
- // jump two lines to the data
- sc.nextLine(); sc.nextLine();
-
- // Read the first, second and fourth columns. Ignoring everything else.
- // Allocate necessry data structures for creating Score objects
- ArrayList<Float> scores = new ArrayList<Float>();
- List<Range> rangeHolder = new ArrayList<Range>();
- String s = "null";
- while (true) {
- s = sc.next();
- if (java.util.regex.Pattern.matches("^[\\.)(]{2,}$", s)) break;
- if (!sc.hasNextLine()) break;
- int t = sc.nextInt();
- rangeHolder.add(new Range(Integer.parseInt(s), t));
- sc.next();
- scores.add(sc.nextFloat());
- sc.nextLine();
- }
- sc.close();
-
- // Update the first ScoreHolder TreeSet<Score> element
- assert (rangeHolder.size() == scores.size());
- TreeSet<Score> sHolder = new TreeSet<Score>();
- for (int i = 0; i < rangeHolder.size(); i++) {
- ArrayList<Float> singleS = new ArrayList<Float>(Arrays.asList(scores.get(i)));
- TreeSet<Range> singleR = new TreeSet<Range>(Arrays.asList(rangeHolder.get(i)));
- sHolder.add(new Score(AlifoldResult.alifoldSeq, singleS, singleR));
- }
-
- data.set(0, sHolder);
-
- return new ScoreManager(new RNAStruct(structs, data));
- }
-
- private static RNAOut identify(String token) {
- if (Pattern.matches(seqP, token)) {
- return RNAOut.SEQ;
- } else if (Pattern.matches(structP, token)) {
- return RNAOut.STRUCT;
- } else if (Pattern.matches(energyP, token)) {
- return RNAOut.ENERGY;
- } else if (Pattern.matches(freqP, token)) {
- return RNAOut.FREQ;
- }
-
- return RNAOut.OTHER;
- }
-
- private static AlifoldLine identifyLine(String line) {
-
- for (AlifoldLine il : AlifoldLine.values()) {
- if (Pattern.matches(il.regex, line)) return il;
- }
- return AlifoldLine.OTHER;
- }
-
- static enum AlifoldLine {
- stdStruct (stdStructP),
- justStruct (justStructP),
- stochBTStruct (stochBTStructP),
- PStruct (PStructP),
- centStruct (centStructP),
- MEAStruct (MEAStructP),
- freeEnergy (freeEnergyP),
- ensembleFreq (ensembleFreqP),
- alignment (alignmentP),
- OTHER (".*");
-
- String regex;
- AlifoldLine(String regex) { this.regex = regex; }
-
- }
-
- //The types of data in an RNAalifold stdout file
- static enum RNAOut {
- SEQ, STRUCT, ENERGY, FREQ, OTHER
- }
-
- //Something to put in the Score objects of the alifold result which gives information
- //about what kind of sequence it is holding in its String Id.
- static enum AlifoldResult {
- alifold, alifoldP, alifoldMEA, alifoldCentroid, alifoldStochBT, alifoldSeq, alifoldMetadata
- }
-
-
-
- // Print the full regex Strings for testing
- public static void main(String[] args) {
- for (AlifoldLine l : AlifoldLine.values()) {
- System.out.println(l.toString() + ": " + l.regex.replace("^","").replace("$",""));
- }
- }
-
-
-
-}
+package compbio.data.sequence;\r
+\r
+import java.io.BufferedReader;\r
+import java.io.InputStream;\r
+import java.io.InputStreamReader;\r
+import java.io.IOException;\r
+import java.util.ArrayList;\r
+import java.util.Arrays;\r
+import java.util.List;\r
+import java.util.Scanner;\r
+import java.util.TreeSet;\r
+import java.util.regex.Pattern;\r
+\r
+import org.apache.log4j.Logger;\r
+\r
+import compbio.runner.structure.RNAalifold;\r
+\r
+// Utility class for reading alifold output\r
+\r
+public class RNAStructReader {\r
+\r
+ private static Logger log = Logger.getLogger(RNAStructReader.class);\r
+ \r
+ // Whitespace patterns\r
+ static String s = "[+\\s=]+";\r
+ static String bracket = "\\(|\\)|\\{|\\}|\\[|\\]";\r
+ static String notData = "[\\s=+]+";\r
+\r
+ // RNAOut data type patterns \r
+ static String seqP = "[_\\-a-zA-Z]{2,}"; // Has to match --mis output aswell (not just ACGU_)\r
+ static String structP = "[\\.)({}\\[\\],]{2,}";\r
+ static String floatP = "-?\\d+\\.\\d*(e[+\\-]\\d+)?";\r
+ static String energyP = "-?[0-9]*\\.?[0-9]{2}";\r
+ static String freqP = "^-?\\d\\.\\d{6,}(e[+\\-]\\d+)?$";\r
+ \r
+ // alifold out line patterns\r
+ static String ps = "\\s*";\r
+ static String alignmentP = "^"+seqP+ps+"$";\r
+ static String stdStructP = "^"+structP+s+"\\("+ps+floatP+s+floatP+s+floatP+ps+"\\)"+ps+"$";\r
+ static String justStructP = "^"+structP+ps+"$";\r
+ static String stochBTStructP = "^"+structP+s+floatP+s+floatP+ps+"$";\r
+ static String PStructP = "^"+structP+s+"\\["+ps+floatP+ps+"\\]"+ps+"$";\r
+ static String centStructP = "^"+structP+s+floatP+ps+"\\{"+ps+floatP+s+floatP+ps+"\\}"+ps+"$";\r
+ static String MEAStructP = "^"+structP+s+"\\{"+ps+floatP+s+"MEA="+floatP+ps+"\\}"+ps+"$";\r
+ static String freeEnergyP = "^"+ps+"free energy of ensemble"+ps+"="+ps+floatP+ps+"kcal/mol"+ps+"$";\r
+ static String ensembleFreqP = "^"+ps+"frequency of mfe structure in ensemble "+floatP+ps+"$";\r
+\r
+ public static RNAStructScoreManager readRNAStructStream(InputStream stdout)\r
+ throws IOException {\r
+ \r
+ String error = "Error in parsing alifold stdout file: ";\r
+ // The Lists required to construct a ScoreManager Using the new constructor\r
+ List<String> structs = new ArrayList<String>();\r
+ List<TreeSet<Score>> data = new ArrayList<TreeSet<Score>>();\r
+\r
+ // Allocate necessry data structures for creating Score objects\r
+ ArrayList<Float> scores = new ArrayList<Float>();\r
+\r
+ BufferedReader reader = new BufferedReader(new InputStreamReader(stdout));\r
+ // The first 2 lines of the alifold stdout file are always the same format\r
+ String fline = reader.readLine();\r
+ assert (Pattern.matches(AlifoldLine.alignment.regex, fline)) :\r
+ error + "Sequence Alignment Expected";\r
+ structs.add(fline.trim());\r
+ data.add(newEmptyScore(AlifoldResult.alifoldSeq));\r
+ \r
+ fline = reader.readLine();\r
+ assert (Pattern.matches(AlifoldLine.stdStruct.regex, fline)) :\r
+ error + "Consensus Structure and Energy Expected";\r
+ Scanner sc = new Scanner(fline);\r
+ structs.add(sc.next());\r
+ for (int i = 0; i < 3; i++) {\r
+ scores.add(Float.parseFloat(sc.findInLine(floatP)));\r
+ }\r
+ data.add(newSetScore(AlifoldResult.alifold, scores));\r
+ \r
+ // Now the alifold stdout file formats diverge based on arguments\r
+ fline = reader.readLine();\r
+ String sline;\r
+ Scanner nsc = null;\r
+ while ( fline != null) {\r
+ scores.clear();\r
+ AlifoldLine ftype = identifyLine(fline);\r
+ sline = reader.readLine(); // Look ahead\r
+ sc = new Scanner(fline);\r
+ if (sline != null) nsc = new Scanner(sline);\r
+\r
+ if (ftype.equals(AlifoldLine.PStruct)) {\r
+ // The -p or --MEA option is specified\r
+ // The next line should always be frequency of mfe structure\r
+ assert ( sline != null && Pattern.matches(AlifoldLine.ensembleFreq.regex, sline)) :\r
+ error + "Expected frequency of mfe structure";\r
+ structs.add(sc.next());\r
+ scores.add(Float.parseFloat(sc.findInLine(floatP)));\r
+ scores.add(Float.parseFloat(nsc.findInLine(floatP)));\r
+ data.add(newSetScore(AlifoldResult.alifoldP, scores));\r
+ // Jump line\r
+ sline = reader.readLine();\r
+ }\r
+ else if (ftype.equals(AlifoldLine.centStruct)) {\r
+ structs.add(sc.next());\r
+ for (int i = 0; i < 3; i++) {\r
+ scores.add(Float.parseFloat(sc.findInLine(floatP)));\r
+ }\r
+ data.add(newSetScore(AlifoldResult.alifoldCentroid, scores));\r
+ }\r
+ else if (ftype.equals(AlifoldLine.MEAStruct)) {\r
+ structs.add(sc.next());\r
+ for (int i = 0; i < 2; i++) {\r
+ scores.add(Float.parseFloat(sc.findInLine(floatP)));\r
+ }\r
+ data.add(newSetScore(AlifoldResult.alifoldMEA, scores));\r
+ }\r
+ else if (ftype.equals(AlifoldLine.justStruct)) {\r
+ structs.add(sc.next());\r
+ data.add(newEmptyScore(AlifoldResult.alifoldStochBT));\r
+ }\r
+ else if (ftype.equals(AlifoldLine.stochBTStruct)) {\r
+ structs.add(sc.next());\r
+ scores.add(sc.nextFloat());\r
+ scores.add(sc.nextFloat());\r
+ data.add(newSetScore(AlifoldResult.alifoldStochBT, scores));\r
+ }\r
+ else if (ftype.equals(AlifoldLine.freeEnergy)) {\r
+ assert (sline != null \r
+ && Pattern.matches(AlifoldLine.ensembleFreq.regex, sline)) :\r
+ error + "Found 'freeEnergy' line on its own";\r
+ structs.add("Free energy of ensemble (kcal/mol) followed by "\r
+ + "frequency of mfe structure in ensemble");\r
+ scores.add(Float.parseFloat(sc.findInLine(floatP)));\r
+ scores.add(Float.parseFloat(nsc.findInLine(floatP)));\r
+ data.add(newSetScore(AlifoldResult.alifoldMetadata, scores));\r
+ // jump line\r
+ sline = reader.readLine();\r
+ }\r
+ \r
+\r
+ assert(!ftype.equals(AlifoldLine.ensembleFreq)) :\r
+ error + "Wasn't expecting 'frequency of mfe structure'!";\r
+ assert(!ftype.equals(AlifoldLine.stdStruct)) :\r
+ error + "'Standard output' line at a place other than line 2!";\r
+ assert(!ftype.equals(AlifoldLine.alignment)) :\r
+ error + "Wasn't expecting an alignment sequence!";\r
+ assert(!ftype.equals(AlifoldLine.OTHER)) :\r
+ error + "Wasn't expecting this whatever it is: " + fline;\r
+ if (Pattern.matches("^\\s*$", fline)) {\r
+ log.warn("While parsing alifold stdout: A line is either empty or"\r
+ + " contains only whitespace");\r
+ }\r
+ \r
+ fline = sline;\r
+ }\r
+ \r
+ sc.close();\r
+ if (nsc != null) nsc.close();\r
+ \r
+ return new RNAStructScoreManager(structs, data);\r
+ }\r
+ \r
+ // Just for the purpose of creating nee TreeSet<Score> objects of length one\r
+ // for adding to a 'data' list to make a ScoreManager\r
+ private static TreeSet<Score> newSetScore(Enum<?> res, List<Float> scores) {\r
+ // first convert List<Float> to float[]\r
+ float[] scoresf = new float[scores.size()];\r
+ Float f;\r
+ for (int i = 0; i < scoresf.length; i++) {\r
+ f = scores.get(i);\r
+ scoresf[i] = ( f != null ? f : Float.NaN);\r
+ }\r
+ return new TreeSet<Score>(Arrays.asList(new Score(res, scoresf)));\r
+ }\r
+\r
+ // A method just for the purpose of neatly creating Almost Empty score objects\r
+ // that can't be null\r
+ public static TreeSet<Score> newEmptyScore(Enum<?> res) {\r
+ return new TreeSet<Score>(Arrays.asList(new Score(res, new float[0])));\r
+ }\r
+\r
+ public static RNAStructScoreManager readRNAStructStream(InputStream stdout, \r
+ InputStream alifold) throws IOException {\r
+ \r
+ // The Lists required to construct a ScoreManager Using the new constructor\r
+ List<String> structs;\r
+ List<TreeSet<Score>> data; \r
+ \r
+ // Get a ScoreManager that takes the std output but ignores alifold.out (-p)\r
+ RNAStructScoreManager stdSM = readRNAStructStream(stdout);\r
+ \r
+ // Unpack this into the structs and data lists\r
+ structs = stdSM.getStructs();\r
+ data = stdSM.getData();\r
+ \r
+ // Now parse alifold.out\r
+ Scanner sc = new Scanner(alifold);\r
+ sc.useDelimiter("[\\s%]+");\r
+ \r
+ // jump two lines to the data \r
+ sc.nextLine(); sc.nextLine();\r
+ \r
+ // Read the first, second and fourth columns. Ignoring everything else.\r
+ // Allocate necessry data structures for creating Score objects\r
+ ArrayList<Float> scores = new ArrayList<Float>();\r
+ List<Range> rangeHolder = new ArrayList<Range>();\r
+ String s = "null";\r
+ while (true) {\r
+ s = sc.next();\r
+ if (java.util.regex.Pattern.matches("^[\\.)(]{2,}$", s)) break;\r
+ if (!sc.hasNextLine()) break;\r
+ int t = sc.nextInt();\r
+ rangeHolder.add(new Range(Integer.parseInt(s), t));\r
+ sc.next();\r
+ scores.add(sc.nextFloat());\r
+ sc.nextLine();\r
+ }\r
+ sc.close();\r
+ \r
+ // Update the first ScoreHolder TreeSet<Score> element\r
+ assert (rangeHolder.size() == scores.size());\r
+ TreeSet<Score> sHolder = new TreeSet<Score>();\r
+ for (int i = 0; i < rangeHolder.size(); i++) {\r
+ ArrayList<Float> singleS = new ArrayList<Float>(Arrays.asList(scores.get(i)));\r
+ TreeSet<Range> singleR = new TreeSet<Range>(Arrays.asList(rangeHolder.get(i)));\r
+ sHolder.add(new Score(AlifoldResult.alifoldSeq, singleS, singleR));\r
+ }\r
+ \r
+ data.set(0, sHolder);\r
+ \r
+ return new RNAStructScoreManager(structs, data);\r
+ }\r
+\r
+ private static RNAOut identify(String token) {\r
+ if (Pattern.matches(seqP, token)) {\r
+ return RNAOut.SEQ;\r
+ } else if (Pattern.matches(structP, token)) {\r
+ return RNAOut.STRUCT;\r
+ } else if (Pattern.matches(energyP, token)) {\r
+ return RNAOut.ENERGY;\r
+ } else if (Pattern.matches(freqP, token)) {\r
+ return RNAOut.FREQ;\r
+ }\r
+ \r
+ return RNAOut.OTHER;\r
+ }\r
+ \r
+ private static AlifoldLine identifyLine(String line) {\r
+ \r
+ for (AlifoldLine il : AlifoldLine.values()) {\r
+ if (Pattern.matches(il.regex, line)) return il;\r
+ }\r
+ return AlifoldLine.OTHER;\r
+ }\r
+ \r
+ static enum AlifoldLine {\r
+ stdStruct (stdStructP),\r
+ justStruct (justStructP),\r
+ stochBTStruct (stochBTStructP),\r
+ PStruct (PStructP),\r
+ centStruct (centStructP),\r
+ MEAStruct (MEAStructP),\r
+ freeEnergy (freeEnergyP),\r
+ ensembleFreq (ensembleFreqP),\r
+ alignment (alignmentP), \r
+ OTHER (".*");\r
+ \r
+ String regex;\r
+ AlifoldLine(String regex) { this.regex = regex; }\r
+\r
+ }\r
+ \r
+ //The types of data in an RNAalifold stdout file\r
+ static enum RNAOut {\r
+ SEQ, STRUCT, ENERGY, FREQ, OTHER\r
+ }\r
+\r
+ //Something to put in the Score objects of the alifold result which gives information\r
+ //about what kind of sequence it is holding in its String Id.\r
+ static enum AlifoldResult {\r
+ alifold, alifoldP, alifoldMEA, alifoldCentroid, alifoldStochBT, alifoldSeq, alifoldMetadata\r
+ }\r
+ \r
+ \r
+\r
+ // Print the full regex Strings for testing \r
+ public static void main(String[] args) {\r
+ for (AlifoldLine l : AlifoldLine.values()) {\r
+ System.out.println(l.toString() + ": " + l.regex.replace("^","").replace("$",""));\r
+ }\r
+ }\r
+ \r
+\r
+ \r
+} \r
git://source.jalview.org / jabaws.git / blobdiff