+++ /dev/null
-package compbio.data.sequence;
-
-import java.util.List;
-import java.util.Iterator;
-import java.util.Set;
-import java.util.TreeSet;
-import java.util.List;
-import java.util.ArrayList;
-
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-
-import compbio.util.annotation.Immutable;
-import compbio.util.SysPrefs;
-import compbio.data.sequence.Score;
-
-/*
- * RNA secondary structure
- * A class which is essentially just a Pair(List<String>, List<Set<Score>>)
- * For the purpose of creating and retrieving data from ScoreManager Objects
- * which are being used to store RNA folding output
- */
-
-@XmlAccessorType(XmlAccessType.FIELD)
-public final class RNAStruct {
-
- private List<String> structs = new ArrayList<String>();
- private List<TreeSet<Score>> data = new ArrayList<TreeSet<Score>>();
-
-
- public RNAStruct() {
- // default JaxB Constructor
- }
-
- public RNAStruct(List<String> structs, List<TreeSet<Score>> data) {
- assert(structs.size() == data.size());
- this.structs = structs;
- this.data = data;
- }
-
- public List<String> getStructs() {
- return structs;
- }
-
- public List<TreeSet<Score>> getData() {
- return data;
- }
-
- // Send this data Structure back to something approximating the stdoutFile
- // with extra information from alifold.out
- @Override
- public String toString() {
- String out = "";
- // The first objects hold the Consensus Alignment and the alifold.out info
- out += structs.get(0) + SysPrefs.newlinechar;
-
- // Now the rest of the structures with energies/frequencies
- for (int i = 1; i < structs.size(); i++) {
- out = out + structs.get(i).toString();
-
- if (data.get(i).first().getScores().size() > 0) {
- List<Float> scores = data.get(i).first().getScores();
- if (scores.size() >= 3) {
- out = out + " (" + scores.get(0).toString() + " = "
- + scores.get(1).toString() + " + " + scores.get(2).toString()
- + ")" + SysPrefs.newlinechar;
- }
- else if (data.get(i).first().getMethod().equals("alifoldMEA")) {
- out = out + " { " + scores.get(0).toString() + " MEA="
- + scores.get(1).toString() + "}" + SysPrefs.newlinechar;
- }
- else if (scores.size() >= 2) {
- out = out + " [" + scores.get(0).toString() + ", "
- + scores.get(1).toString() + "]" + SysPrefs.newlinechar;
-
- }
- } else out += SysPrefs.newlinechar;
- }
- if (data.get(0).first().getScores().size() > 0) {
- Iterator<Score> iScores = data.get(0).iterator();
- out += "Base Pairings followed by probability" + SysPrefs.newlinechar;
- for (int i = 0; i < data.get(0).size(); i++) {
- Score s = iScores.next();
- Range r = s.getRanges().first();
- Float score = s.getScores().get(0);
- out += String.format("%4d %4d %.1f%n", r.getFrom(), r.getTo(),
- score);
- }
- }
-
- return out;
- }
-
- @Override
- public boolean equals(Object obj) {
- if (obj == null) {
- return false;
- }
- if (!(obj instanceof RNAStruct)) {
- return false;
- }
- RNAStruct other = (RNAStruct) obj;
- if (structs == null) {
- if (other.structs != null) {
- return false;
- }
- } else if (!structs.equals(other.structs))
- return false;
- if (data == null) {
- if (other.data != null)
- return false;
- } else if (!data.equals(other.data))
- return false;
-
- return true;
- }
-}
-
-
-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
--- /dev/null
+package compbio.data.sequence;\r
+\r
+\r
+import java.io.IOException;\r
+import java.io.Writer;\r
+import java.util.ArrayList;\r
+import java.util.Iterator;\r
+import java.util.List;\r
+import java.util.Map;\r
+import java.util.Set;\r
+import java.util.TreeMap;\r
+import java.util.TreeSet;\r
+\r
+import javax.xml.bind.annotation.XmlAccessType;\r
+import javax.xml.bind.annotation.XmlAccessorType;\r
+import javax.xml.bind.annotation.XmlTransient;\r
+\r
+import compbio.data.sequence.ScoreManager.ScoreHolder;\r
+import compbio.util.SysPrefs;\r
+\r
+@XmlAccessorType(XmlAccessType.FIELD)\r
+public class RNAStructScoreManager extends ScoreManager {\r
+\r
+ \r
+ private RNAStructScoreManager() {\r
+ //Default JAXB constructor\r
+ }\r
+ \r
+\r
+ public RNAStructScoreManager(List<String> structs, List<TreeSet<Score>> data) {\r
+ assert(structs.size() == data.size());\r
+ \r
+ List<ScoreHolder> seqScores = new ArrayList<ScoreHolder>();\r
+ \r
+ for (int i = 0; i < structs.size(); i++) {\r
+ seqScores.add(new ScoreHolder(structs.get(i), data.get(i)));\r
+ }\r
+ this.seqScores = seqScores;\r
+ }\r
+ \r
+ // I put this in purely because it mirrors a method in ScoreManager, not because I need it :/\r
+ public static RNAStructScoreManager newInstance(List<String> structs, List<TreeSet<Score>> data) {\r
+ return new RNAStructScoreManager(structs, data);\r
+ }\r
+ \r
+ public List<String> getStructs() {\r
+ List<String> structs = new ArrayList<String>();\r
+ for (ScoreHolder sch : this.seqScores) {\r
+ structs.add(sch.id);\r
+ }\r
+ return structs;\r
+ }\r
+ \r
+ public List<TreeSet<Score>> getData() {\r
+ List<TreeSet<Score>> data = new ArrayList<TreeSet<Score>>();\r
+ for (ScoreHolder sch : this.seqScores) {\r
+ data.add(sch.scores);\r
+ }\r
+ return data;\r
+ }\r
+\r
+ // Send this data Structure back to something approximating the stdoutFile\r
+ // with extra information from alifold.out\r
+ @Override\r
+ public String toString() {\r
+ String out = "";\r
+ // The first objects hold the Consensus Alignment and the alifold.out info\r
+ out += this.getStructs().get(0) + SysPrefs.newlinechar;\r
+\r
+ // Now the rest of the structures with energies/frequencies\r
+ for (int i = 1; i < this.getStructs().size(); i++) {\r
+ out = out + this.getStructs().get(i).toString();\r
+\r
+ if (this.getData().get(i).first().getScores().size() > 0) {\r
+ List<Float> scores = this.getData().get(i).first().getScores();\r
+ if (scores.size() >= 3) {\r
+ out = out + " (" + scores.get(0).toString() + " = " \r
+ + scores.get(1).toString() + " + " + scores.get(2).toString()\r
+ + ")" + SysPrefs.newlinechar;\r
+ }\r
+ else if (this.getData().get(i).first().getMethod().equals("alifoldMEA")) {\r
+ out = out + " { " + scores.get(0).toString() + " MEA=" \r
+ + scores.get(1).toString() + "}" + SysPrefs.newlinechar;\r
+ }\r
+ else if (scores.size() >= 2) {\r
+ out = out + " [" + scores.get(0).toString() + ", " \r
+ + scores.get(1).toString() + "]" + SysPrefs.newlinechar;\r
+\r
+ }\r
+ } else out += SysPrefs.newlinechar; \r
+ }\r
+ if (this.getData().get(0).first().getScores().size() > 0) {\r
+ Iterator<Score> iScores = this.getData().get(0).iterator();\r
+ out += "Base Pairings followed by probability" + SysPrefs.newlinechar;\r
+ for (int i = 0; i < this.getData().get(0).size(); i++) {\r
+ Score s = iScores.next();\r
+ Range r = s.getRanges().first();\r
+ Float score = s.getScores().get(0);\r
+ out += String.format("%4d %4d %.1f%n", r.getFrom(), r.getTo(),\r
+ score);\r
+ }\r
+ }\r
+\r
+\r
+ return out;\r
+ }\r
+\r
+ @Override \r
+ public boolean equals(Object obj) {\r
+ if (obj == null) {\r
+ return false;\r
+ }\r
+ if (!(obj instanceof RNAStructScoreManager)) {\r
+ return false;\r
+ }\r
+ RNAStructScoreManager other = (RNAStructScoreManager) obj;\r
+ if (this.getStructs() == null) {\r
+ if (other.getStructs() != null) {\r
+ return false;\r
+ }\r
+ } else if (!this.getStructs().equals(other.getStructs()))\r
+ return false;\r
+ if (this.getData() == null) {\r
+ if (other.getData() != null)\r
+ return false;\r
+ } else if (!this.getData().equals(other.getData()))\r
+ return false;\r
+\r
+ return true;\r
+ }\r
+}\r
-package compbio.runner.structure;
-
-
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.util.Arrays;
-import java.util.List;
-
-
-
-
-
-import org.apache.log4j.Logger;
-
-import compbio.data.sequence.ScoreManager;
-import compbio.data.sequence.RNAStruct;
-import compbio.data.sequence.UnknownFileFormatException;
-import compbio.engine.client.PipedExecutable;
-import compbio.engine.client.SkeletalExecutable;
-import compbio.metadata.ResultNotAvailableException;
-import compbio.runner.Util;
-
-
-import compbio.engine.client.CommandBuilder;
-
-public class RNAalifold extends SkeletalExecutable<RNAalifold>
- implements PipedExecutable<RNAalifold> {
-
-
- private static Logger log = Logger.getLogger(RNAalifold.class);
-
- // May not be necessary as defult is "<space>" but still dont know
- // How to deal with different key value separators for different params
- public static final String KEY_VALUE_SEPARATOR = " ";
-
- public RNAalifold() {
- super(KEY_VALUE_SEPARATOR);
- }
-
- @Override
- public RNAalifold setOutput(String outFile) {
- super.setOutput(outFile);
- return this;
- }
-
- @Override
- public RNAalifold setInput(String inFile) {
- cbuilder.setLast(inFile);
- super.setInput(inFile);
- return this;
- }
-
- @SuppressWarnings("unchecked")
- @Override
- public Class<RNAalifold> getType() {
- return (Class<RNAalifold>) this.getClass();
- }
-
- @SuppressWarnings("unchecked")
- @Override
- // PlaceHolder method
- public ScoreManager getResults(String workDirectory)
- throws ResultNotAvailableException {
- try {
- return Util.readRNAStruct(workDirectory, getOutput());
-
- } catch (FileNotFoundException e) {
- log.error(e.getMessage(), e.getCause());
- throw new ResultNotAvailableException(e);
- } catch (IOException e) {
- log.error(e.getMessage(), e.getCause());
- throw new ResultNotAvailableException(e);
- }
- }
-
-
- // the new currently used methods for reading are found in
- // - compbio.data.sequence.SequenceUtil and
- // - compbio.runner.Util
-
- // Simple and generic methods for reading a whole file
-// private static String readRNAStruct(String workDirectory,
-// String structFile) throws IOException, FileNotFoundException {
-// assert !compbio.util.Util.isEmpty(workDirectory);
-// assert !compbio.util.Util.isEmpty(structFile);
-// File sfile = new File(compbio.engine.client.Util.getFullPath(
-// workDirectory, structFile));
-// log.trace("RNAALIFOLD OUTPUT FILE PATH: " + sfile.getAbsolutePath());
-// if(!(sfile.exists() && sfile.length() > 0)) {
-// throw new FileNotFoundException("Result for the jobId "
-// + workDirectory + "with file name " + structFile
-// + " is not found!");
-// }
-// return readFile(sfile);
-// }
-//
-// private static BufferedReader input;
-// public static String readFile(File inputFile) throws
-// FileNotFoundException, IOException {
-//
-// input = new BufferedReader(new FileReader(inputFile));
-//
-// String file = new String();
-// String line = new String();
-//
-// while (true) {
-// line = input.readLine();
-//
-// if (line != null) {
-// file = file + line + "\r\n";
-// } else break;
-// }
-// // Close file
-// input.close();
-// return file;
-// }
-
-}
+package compbio.runner.structure;\r
+\r
+\r
+import java.io.FileNotFoundException;\r
+import java.io.IOException;\r
+import java.util.Arrays;\r
+import java.util.List;\r
+\r
+\r
+\r
+\r
+\r
+import org.apache.log4j.Logger;\r
+\r
+import compbio.data.sequence.ScoreManager;\r
+import compbio.data.sequence.RNAStructScoreManager;\r
+import compbio.data.sequence.UnknownFileFormatException;\r
+import compbio.engine.client.PipedExecutable;\r
+import compbio.engine.client.SkeletalExecutable;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.runner.Util;\r
+\r
+\r
+import compbio.engine.client.CommandBuilder;\r
+\r
+public class RNAalifold extends SkeletalExecutable<RNAalifold> \r
+ implements PipedExecutable<RNAalifold> {\r
+ \r
+ \r
+ private static Logger log = Logger.getLogger(RNAalifold.class);\r
+\r
+ // May not be necessary as defult is "<space>" but still dont know\r
+ // How to deal with different key value separators for different params\r
+ public static final String KEY_VALUE_SEPARATOR = " ";\r
+ \r
+ public RNAalifold() {\r
+ super(KEY_VALUE_SEPARATOR);\r
+ }\r
+ \r
+ @Override\r
+ public RNAalifold setOutput(String outFile) {\r
+ super.setOutput(outFile);\r
+ return this;\r
+ }\r
+ \r
+ @Override\r
+ public RNAalifold setInput(String inFile) {\r
+ cbuilder.setLast(inFile);\r
+ super.setInput(inFile);\r
+ return this;\r
+ }\r
+ \r
+ @SuppressWarnings("unchecked")\r
+ @Override\r
+ public Class<RNAalifold> getType() {\r
+ return (Class<RNAalifold>) this.getClass();\r
+ }\r
+ \r
+ @SuppressWarnings("unchecked")\r
+ @Override\r
+ public RNAStructScoreManager getResults(String workDirectory)\r
+ throws ResultNotAvailableException {\r
+ try {\r
+ return Util.readRNAStruct(workDirectory, getOutput());\r
+ \r
+ } catch (FileNotFoundException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ } catch (IOException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ }\r
+ }\r
+\r
+}\r
-package compbio.runner.structure;
-
-import static org.testng.Assert.assertFalse;
-import static org.testng.Assert.assertNotNull;
-import static org.testng.Assert.assertTrue;
-import static org.testng.Assert.fail;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-import java.util.Map;
-
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.ValidationException;
-
-import org.apache.log4j.Level;
-import org.apache.log4j.Logger;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import compbio.data.sequence.ScoreManager;
-import compbio.engine.Configurator;
-import compbio.engine.client.ConfiguredExecutable;
-import compbio.engine.client.Executable.ExecProvider;
-import compbio.engine.conf.RunnerConfigMarshaller;
-import compbio.engine.local.ExecutableWrapper;
-import compbio.engine.local.LocalRunner;
-import compbio.metadata.AllTestSuit;
-import compbio.metadata.JobExecutionException;
-import compbio.metadata.JobSubmissionException;
-import compbio.metadata.Option;
-import compbio.metadata.Parameter;
-import compbio.metadata.Preset;
-import compbio.metadata.PresetManager;
-import compbio.metadata.ResultNotAvailableException;
-import compbio.metadata.RunnerConfig;
-import compbio.runner.OptionCombinator;
-import compbio.runner.structure.RNAalifold;
-import compbio.util.FileUtil;
-
-
-public class RNAalifoldParametersTester {
-
-
- // should be: AllTestSuit.TEST_DATA_PATH + "RNAalifoldParameters.xml"
- static final String rnaalifoldConfigFile =
- AllTestSuit.TEST_DATA_PATH + "RNAalifoldParameters.xml";
- public static String test_outfile = "rnaalifold.out.txt";
-
- private static Logger log = Logger
- .getLogger(AllTestSuit.RUNNER_TEST_LOGGER);
-
- static {
- log.setLevel(Level.INFO);
- }
-
- RunnerConfig<RNAalifold> rnaalifoldConfig = null;
- OptionCombinator rnaalifoldOpc = null;
-
- @BeforeMethod(groups = { AllTestSuit.test_group_runner })
- @SuppressWarnings("unchecked")
- public void setup() {
- try {
- RunnerConfigMarshaller<RNAalifold> rnaalifoldmarsh =
- new RunnerConfigMarshaller<RNAalifold>(RunnerConfig.class);
- rnaalifoldConfig = rnaalifoldmarsh.read(new FileInputStream(new File(
- rnaalifoldConfigFile)), RunnerConfig.class);
- // set Name value separator
- rnaalifoldConfig.setPrmSeparator(" ");
- rnaalifoldOpc = new OptionCombinator(rnaalifoldConfig);
-
-
-
- } catch (JAXBException e) {
- e.printStackTrace();
- fail(e.getLocalizedMessage());
- } catch (FileNotFoundException e) {
- e.printStackTrace();
- fail(e.getLocalizedMessage());
- }
- }
-
- @Test
- public void testConfiguration() {
- try {
- this.rnaalifoldConfig.validate();
- } catch (ValidationException e) {
- e.printStackTrace();
- fail(e.getLocalizedMessage());
- } catch (IllegalStateException e) {
- e.printStackTrace();
- fail(e.getLocalizedMessage());
- }
- }
-
- @Test(groups = { AllTestSuit.test_group_runner })
- public void testDefaultParameters() {
- RNAalifold rnaalifold = new RNAalifold();
- rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput(test_outfile);
-
- try {
- // For local execution use relavive
- ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator
- .configureExecutable(rnaalifold);
- LocalRunner lr = new LocalRunner(confRNAalifold);
- lr.executeJob();
- confRNAalifold = (ConfiguredExecutable<RNAalifold>) lr.waitForResult();
- assertNotNull(confRNAalifold.getResults());
- } catch (JobSubmissionException e) {
- e.printStackTrace();
- fail(e.getLocalizedMessage());
- } catch (JobExecutionException e) {
- e.printStackTrace();
- fail(e.getLocalizedMessage());
- } catch (ResultNotAvailableException e) {
- e.printStackTrace();
- fail(e.getLocalizedMessage());
- }
- }
-
-
-
- @Test
- public void testOptions() {
- // populate list of incompatable pairs by their names. todo
- List<List<String>> failPairs = new ArrayList<List<String>>();
-
-
- // test the parameters without -g option
- test(removeParam(rnaalifoldOpc.getAllOptions(), "G-Quadruplex"));
- // now test without -c option
- test(removeParam(rnaalifoldOpc.getAllOptions(), "Circular"));
- }
-
-
- // Prints all the incompatible option pairs
- // (-c, -g) and (-p, -p0)
-
- @Test
- public void testOptionPairs() throws ResultNotAvailableException {
- List<Option<?>> pair = new ArrayList<Option<?>>();
- List<Option<?>> options = rnaalifoldOpc.getAllOptions();
- List<List<String>> failedOptionPairs = new ArrayList<List<String>>();
-
- boolean failed = true;
- for (int i = 0; i<options.size(); i++) {
- for (int j = i; j<options.size(); j++) {
- if (i != j) {
- pair.clear();
- pair.add(options.get(i)); pair.add(options.get(j));
- List<String> args = rnaalifoldOpc.argumentsToCommandString(pair);
- try {
- failed = singleRun(args);
- } catch (ResultNotAvailableException e) {
- System.out.println("Results not available: " + e.getMessage());
- failed = true;
- } catch (JobSubmissionException e) {
- e.printStackTrace();
- fail(e.getLocalizedMessage());
- } catch (JobExecutionException e) {
- e.printStackTrace();
- fail(e.getLocalizedMessage());
- } catch (IOException e) {
- e.printStackTrace();
- fail(e.getLocalizedMessage());
- }
- if (failed == true) {
- failedOptionPairs.add(args);
- }
- }
- }
- }
- System.out.println("failedOptionPairs: " + failedOptionPairs);
-
- }
-
- // tests for incompatible Pairs of Parameters
- // there are none however the --betascale parameter requires -p
-
- @Test
- public void testParameterPairs() throws ResultNotAvailableException {
- List<Parameter<?>> pair = new ArrayList<Parameter<?>>();
- List<Parameter<?>> Parameters = rnaalifoldOpc.getAllParameters();
- List<List<String>> failedParameterPairs = new ArrayList<List<String>>();
-
-
- boolean failed = true;
- for (int i = 0; i<Parameters.size(); i++) {
- for (int j = i; j<Parameters.size(); j++) {
- if (i != j) {
- pair.clear();
- pair.add(Parameters.get(i)); pair.add(Parameters.get(j));
- List<String> args = rnaalifoldOpc.argumentsToCommandString(pair);
- args.add("-p"); // --betascale requires -p
- try {
- failed = singleRun(args);
- } catch (ResultNotAvailableException e) {
- System.out.println("Results not available: " + e.getMessage());
- failed = true;
- } catch (JobSubmissionException e) {
- e.printStackTrace();
- fail(e.getLocalizedMessage());
- } catch (JobExecutionException e) {
- e.printStackTrace();
- fail(e.getLocalizedMessage());
- } catch (IOException e) {
- e.printStackTrace();
- fail(e.getLocalizedMessage());
- }
- if (failed == true) {
- failedParameterPairs.add(args);
- }
- }
- }
- }
- System.out.println("failedParameterPairs: " + failedParameterPairs);
-
- }
-
-
- // removes an argument from the list by name
- public <U extends Option<?>> List<U> removeParam(List<U> optionList, String name) {
- List<U> newL = new ArrayList<U>();
- for (int i = 0; i < optionList.size(); i++) {
- System.out.println(name.equals(optionList.get(i).getName()));
- if (!name.equals(optionList.get(i).getName())) {
-
- newL.add(optionList.get(i));
- }
-
- }
- return newL;
- }
-
- public <U extends Option<?>> List<U> removeParams(List<U> optionList, List<String> names) {
- for (int i = 0; i < names.size(); i++) {
- optionList = removeParam(optionList, names.get(i));
- }
- return optionList;
- }
-
-
- @Test(groups = { AllTestSuit.test_group_runner })
- public void testParameters() {
- List<Parameter<?>> params = rnaalifoldOpc.getAllParameters();
- System.out.println("param list: " + params);
- Collections.shuffle(params);
- // test with -p for betascale option
- List<String> precursor = new ArrayList<String>();
- precursor.add("-p");
-
- test(params, precursor);
- }
-
- // incompatible pairs of arguments are
- /*
- * the -c and -g options
- * the -d2 option and the -d option
- * the -p and -p0 option
- */
-
- @Test(groups = { AllTestSuit.test_group_runner })
- public void testArguments() {
- List<Option<?>> options = rnaalifoldOpc.getAllOptions();
- options.addAll(rnaalifoldOpc.getAllParameters());
- Collections.shuffle(options);
- test(options);
- }
-
- // This test supercedes the testParameterPair() and testOptionPair()
- // tests by testing all pairs of arguments
-
-
- @Test
- public void testAllPairs() throws ResultNotAvailableException {
- List<Option<?>> pair = new ArrayList<Option<?>>();
- List<Option<?>> options = rnaalifoldOpc.getAllOptions();
-
- // take out -p options so it can be added to all commands later
- // options = removeParam(options, "Partition Function");
-
- options.addAll(rnaalifoldOpc.getAllParameters());
- List<List<String>> failedOptionPairs = new ArrayList<List<String>>();
-
- boolean failed = true;
- for (int i = 0; i<options.size(); i++) {
- for (int j = i; j<options.size(); j++) {
- if (i != j) {
- pair.clear();
- pair.add(options.get(i)); pair.add(options.get(j));
- List<String> args = rnaalifoldOpc.argumentsToCommandString(pair);
- // add -p
- // args.add("-p");
- try {
- failed = singleRun(args);
- } catch (ResultNotAvailableException e) {
- System.out.println("Results not available: " + e.getMessage());
- failed = true;
- } catch (JobSubmissionException e) {
- e.printStackTrace();
- fail(e.getLocalizedMessage());
- } catch (JobExecutionException e) {
- e.printStackTrace();
- fail(e.getLocalizedMessage());
- } catch (IOException e) {
- e.printStackTrace();
- fail(e.getLocalizedMessage());
- }
- if (failed == true) {
- failedOptionPairs.add(args);
- }
- }
- }
- }
- System.out.println("failedOptionPairs: " + failedOptionPairs);
- }
-
- /*
- * This test method stolen from the other parameter testing classes
- * the only purpose of the Collections.shuffle(params) and the for loop
- * is to test giving the executable the parameters in different orders
- * which leads to a lot of (unnecessary?) tests with an argument list
- * as long as this one.
- *
- */
-
-
- void test(List<? extends Option<?>> params) {
- for (int i = 0; i < params.size(); i++) {
- List<String> args = rnaalifoldOpc.argumentsToCommandString(params);
- singleTest(args);
- Collections.shuffle(params);
- }
- log.info("NUMBER OF COMBINATION TESTED: " + params.size());
- }
-
- // because some parameters presuppose the -p option
-
- void test(List<? extends Option<?>> params, List<String> precursor) {
-
- for (int i = 0; i < params.size(); i++) {
- List<String> args = rnaalifoldOpc.argumentsToCommandString(params);
- args.addAll(precursor);
- singleTest(args);
- Collections.shuffle(params);
- }
- log.info("NUMBER OF COMBINATION TESTED: " + params.size());
- }
- @Test
- void singleParamTest() {
- //List<Parameter<?>> params = rnaalifoldOpc.getAllParameters();
- //System.out.println("special: params: " + params);
-
- //List<String> args = rnaalifoldOpc.argumentsToCommandString(params);
- List<String> args = new ArrayList<String>();
- //args.add("-T 37"); args.add("-S 1.07"); args.add("--stochBT_en 10");
- // replace "=" with " " to fail test
- args.add("--MEA=1");
- args.add("-p");
- singleTest(args);
-
- }
-
- void singleTest(List<String> params) {
- try {
- log.info("Using arguments: " + params);
- RNAalifold rnaalifold = new RNAalifold();
- rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput(test_outfile);
-
- ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator
- .configureExecutable(rnaalifold, ExecProvider.Local);
- // Add options to the executable
- confRNAalifold.addParameters(params);
- LocalRunner lr = new LocalRunner(confRNAalifold);
- lr.executeJob();
- confRNAalifold = (ConfiguredExecutable<RNAalifold>) lr.waitForResult();
- assertNotNull(confRNAalifold.getResults(), "results is null");
-
- System.out.println("Results: \n"
- + ((ScoreManager) confRNAalifold.getResults()).asRNAStruct().toString());
-
- File errors = new File(confRNAalifold.getWorkDirectory(),
- ExecutableWrapper.PROC_ERR_FILE);
- if (errors.length() != 0) {
- log.error("PROBLEMS:\n " + FileUtil.readFileToString(errors));
- }
- assertTrue(errors.length() == 0, "Run with arguments : " + params
- + " FAILED!");
- Collections.shuffle(params);
- } catch (JobSubmissionException e) {
- e.printStackTrace();
- fail(e.getLocalizedMessage());
- } catch (JobExecutionException e) {
- e.printStackTrace();
- fail(e.getLocalizedMessage());
- } catch (IOException e) {
- e.printStackTrace();
- fail(e.getLocalizedMessage());
- } catch (ResultNotAvailableException e) {
- e.printStackTrace();
- fail(e.getLocalizedMessage());
- }
- }
-
- /* A version of singleTest that continues running instead of calling
- * fail() when it encounters a problem
- *
- * Used to identify incompatible options and parameters
- * returns -1 on failure
- *
- * Bad Progamming practice?
- */
-
-
- boolean singleRun(List<String> params) throws JobSubmissionException,
- JobExecutionException, IOException, ResultNotAvailableException {
- boolean fail = true;
- log.info("Using arguments: " + params);
- RNAalifold rnaalifold = new RNAalifold();
- rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput(test_outfile);
-
- ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator
- .configureExecutable(rnaalifold, ExecProvider.Local);
- // Add options to the executable
- confRNAalifold.addParameters(params);
- LocalRunner lr = new LocalRunner(confRNAalifold);
- lr.executeJob();
- confRNAalifold = (ConfiguredExecutable<RNAalifold>) lr.waitForResult();
-
- System.out.println("Results: \n"
- + ((ScoreManager) confRNAalifold.getResults()).asRNAStruct().toString());
- if (confRNAalifold.getResults() != null) fail = false;
- File errors = new File(confRNAalifold.getWorkDirectory(),
- ExecutableWrapper.PROC_ERR_FILE);
- if (errors.length() != 0) {
- log.error("PROBLEMS:\n " + FileUtil.readFileToString(errors));
- }
- assertTrue(errors.length() == 0, "Run with arguments : " + params
- + " FAILED!");
- Collections.shuffle(params);
- return fail;
- }
-}
+package compbio.runner.structure;\r
+\r
+import static org.testng.Assert.assertFalse;\r
+import static org.testng.Assert.assertNotNull;\r
+import static org.testng.Assert.assertTrue;\r
+import static org.testng.Assert.fail;\r
+\r
+import java.io.File;\r
+import java.io.FileInputStream;\r
+import java.io.FileNotFoundException;\r
+import java.io.IOException;\r
+import java.util.ArrayList;\r
+import java.util.Collections;\r
+import java.util.List;\r
+import java.util.Map;\r
+\r
+import javax.xml.bind.JAXBException;\r
+import javax.xml.bind.ValidationException;\r
+\r
+import org.apache.log4j.Level;\r
+import org.apache.log4j.Logger;\r
+import org.testng.annotations.BeforeMethod;\r
+import org.testng.annotations.Test;\r
+\r
+import compbio.data.sequence.RNAStructScoreManager;\r
+import compbio.data.sequence.ScoreManager;\r
+import compbio.engine.Configurator;\r
+import compbio.engine.client.ConfiguredExecutable;\r
+import compbio.engine.client.Executable.ExecProvider;\r
+import compbio.engine.conf.RunnerConfigMarshaller;\r
+import compbio.engine.local.ExecutableWrapper;\r
+import compbio.engine.local.LocalRunner;\r
+import compbio.metadata.AllTestSuit;\r
+import compbio.metadata.JobExecutionException;\r
+import compbio.metadata.JobSubmissionException;\r
+import compbio.metadata.Option;\r
+import compbio.metadata.Parameter;\r
+import compbio.metadata.Preset;\r
+import compbio.metadata.PresetManager;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.metadata.RunnerConfig;\r
+import compbio.runner.OptionCombinator;\r
+import compbio.runner.structure.RNAalifold;\r
+import compbio.util.FileUtil;\r
+\r
+\r
+public class RNAalifoldParametersTester {\r
+\r
+ \r
+ // should be: AllTestSuit.TEST_DATA_PATH + "RNAalifoldParameters.xml"\r
+ static final String rnaalifoldConfigFile = \r
+ AllTestSuit.TEST_DATA_PATH + "RNAalifoldParameters.xml";\r
+ public static String test_outfile = "rnaalifold.out.txt";\r
+\r
+ private static Logger log = Logger\r
+ .getLogger(AllTestSuit.RUNNER_TEST_LOGGER);\r
+ \r
+ static {\r
+ log.setLevel(Level.INFO);\r
+ }\r
+ \r
+ RunnerConfig<RNAalifold> rnaalifoldConfig = null;\r
+ OptionCombinator rnaalifoldOpc = null;\r
+ \r
+ @BeforeMethod(groups = { AllTestSuit.test_group_runner })\r
+ @SuppressWarnings("unchecked")\r
+ public void setup() {\r
+ try {\r
+ RunnerConfigMarshaller<RNAalifold> rnaalifoldmarsh = \r
+ new RunnerConfigMarshaller<RNAalifold>(RunnerConfig.class);\r
+ rnaalifoldConfig = rnaalifoldmarsh.read(new FileInputStream(new File(\r
+ rnaalifoldConfigFile)), RunnerConfig.class);\r
+ // set Name value separator\r
+ rnaalifoldConfig.setPrmSeparator(" ");\r
+ rnaalifoldOpc = new OptionCombinator(rnaalifoldConfig);\r
+ \r
+ \r
+ \r
+ } catch (JAXBException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (FileNotFoundException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ }\r
+ \r
+ @Test\r
+ public void testConfiguration() {\r
+ try {\r
+ this.rnaalifoldConfig.validate();\r
+ } catch (ValidationException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (IllegalStateException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ }\r
+\r
+ @Test(groups = { AllTestSuit.test_group_runner })\r
+ public void testDefaultParameters() {\r
+ RNAalifold rnaalifold = new RNAalifold();\r
+ rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput(test_outfile);\r
+\r
+ try {\r
+ // For local execution use relavive\r
+ ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator\r
+ .configureExecutable(rnaalifold);\r
+ LocalRunner lr = new LocalRunner(confRNAalifold);\r
+ lr.executeJob();\r
+ confRNAalifold = (ConfiguredExecutable<RNAalifold>) lr.waitForResult();\r
+ assertNotNull(confRNAalifold.getResults());\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (JobExecutionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ }\r
+ \r
+ \r
+ \r
+ @Test\r
+ public void testOptions() {\r
+ // populate list of incompatable pairs by their names. todo\r
+ List<List<String>> failPairs = new ArrayList<List<String>>();\r
+\r
+ \r
+ // test the parameters without -g option\r
+ test(removeParam(rnaalifoldOpc.getAllOptions(), "G-Quadruplex"));\r
+ // now test without -c option\r
+ test(removeParam(rnaalifoldOpc.getAllOptions(), "Circular"));\r
+ }\r
+ \r
+\r
+ // Prints all the incompatible option pairs \r
+ // (-c, -g) and (-p, -p0)\r
+ \r
+ @Test\r
+ public void testOptionPairs() throws ResultNotAvailableException {\r
+ List<Option<?>> pair = new ArrayList<Option<?>>();\r
+ List<Option<?>> options = rnaalifoldOpc.getAllOptions();\r
+ List<List<String>> failedOptionPairs = new ArrayList<List<String>>();\r
+ \r
+ boolean failed = true;\r
+ for (int i = 0; i<options.size(); i++) {\r
+ for (int j = i; j<options.size(); j++) {\r
+ if (i != j) {\r
+ pair.clear();\r
+ pair.add(options.get(i)); pair.add(options.get(j));\r
+ List<String> args = rnaalifoldOpc.argumentsToCommandString(pair);\r
+ try { \r
+ failed = singleRun(args);\r
+ } catch (ResultNotAvailableException e) {\r
+ System.out.println("Results not available: " + e.getMessage());\r
+ failed = true;\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (JobExecutionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ if (failed == true) {\r
+ failedOptionPairs.add(args);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ System.out.println("failedOptionPairs: " + failedOptionPairs);\r
+ \r
+ }\r
+ \r
+ // tests for incompatible Pairs of Parameters \r
+ // there are none however the --betascale parameter requires -p\r
+ \r
+ @Test\r
+ public void testParameterPairs() throws ResultNotAvailableException {\r
+ List<Parameter<?>> pair = new ArrayList<Parameter<?>>();\r
+ List<Parameter<?>> Parameters = rnaalifoldOpc.getAllParameters();\r
+ List<List<String>> failedParameterPairs = new ArrayList<List<String>>();\r
+ \r
+ \r
+ boolean failed = true;\r
+ for (int i = 0; i<Parameters.size(); i++) {\r
+ for (int j = i; j<Parameters.size(); j++) {\r
+ if (i != j) {\r
+ pair.clear();\r
+ pair.add(Parameters.get(i)); pair.add(Parameters.get(j));\r
+ List<String> args = rnaalifoldOpc.argumentsToCommandString(pair);\r
+ args.add("-p"); // --betascale requires -p\r
+ try { \r
+ failed = singleRun(args);\r
+ } catch (ResultNotAvailableException e) {\r
+ System.out.println("Results not available: " + e.getMessage());\r
+ failed = true;\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (JobExecutionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ if (failed == true) {\r
+ failedParameterPairs.add(args);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ System.out.println("failedParameterPairs: " + failedParameterPairs);\r
+ \r
+ }\r
+ \r
+ \r
+ // removes an argument from the list by name\r
+ public <U extends Option<?>> List<U> removeParam(List<U> optionList, String name) {\r
+ List<U> newL = new ArrayList<U>();\r
+ for (int i = 0; i < optionList.size(); i++) {\r
+ System.out.println(name.equals(optionList.get(i).getName()));\r
+ if (!name.equals(optionList.get(i).getName())) {\r
+ \r
+ newL.add(optionList.get(i));\r
+ }\r
+ \r
+ }\r
+ return newL;\r
+ }\r
+ \r
+ public <U extends Option<?>> List<U> removeParams(List<U> optionList, List<String> names) {\r
+ for (int i = 0; i < names.size(); i++) {\r
+ optionList = removeParam(optionList, names.get(i));\r
+ }\r
+ return optionList;\r
+ }\r
+ \r
+ \r
+ @Test(groups = { AllTestSuit.test_group_runner })\r
+ public void testParameters() {\r
+ List<Parameter<?>> params = rnaalifoldOpc.getAllParameters();\r
+ System.out.println("param list: " + params);\r
+ Collections.shuffle(params);\r
+ // test with -p for betascale option\r
+ List<String> precursor = new ArrayList<String>();\r
+ precursor.add("-p");\r
+ \r
+ test(params, precursor);\r
+ }\r
+ \r
+ // incompatible pairs of arguments are\r
+ /*\r
+ * the -c and -g options\r
+ * the -d2 option and the -d option\r
+ * the -p and -p0 option\r
+ */\r
+\r
+ @Test(groups = { AllTestSuit.test_group_runner })\r
+ public void testArguments() {\r
+ List<Option<?>> options = rnaalifoldOpc.getAllOptions();\r
+ options.addAll(rnaalifoldOpc.getAllParameters());\r
+ Collections.shuffle(options);\r
+ test(options);\r
+ }\r
+ \r
+ // This test supercedes the testParameterPair() and testOptionPair()\r
+ // tests by testing all pairs of arguments\r
+ \r
+ \r
+ @Test\r
+ public void testAllPairs() throws ResultNotAvailableException {\r
+ List<Option<?>> pair = new ArrayList<Option<?>>();\r
+ List<Option<?>> options = rnaalifoldOpc.getAllOptions();\r
+ \r
+ // take out -p options so it can be added to all commands later\r
+ // options = removeParam(options, "Partition Function");\r
+ \r
+ options.addAll(rnaalifoldOpc.getAllParameters());\r
+ List<List<String>> failedOptionPairs = new ArrayList<List<String>>();\r
+ \r
+ boolean failed = true;\r
+ for (int i = 0; i<options.size(); i++) {\r
+ for (int j = i; j<options.size(); j++) {\r
+ if (i != j) {\r
+ pair.clear();\r
+ pair.add(options.get(i)); pair.add(options.get(j));\r
+ List<String> args = rnaalifoldOpc.argumentsToCommandString(pair);\r
+ // add -p\r
+ // args.add("-p");\r
+ try { \r
+ failed = singleRun(args);\r
+ } catch (ResultNotAvailableException e) {\r
+ System.out.println("Results not available: " + e.getMessage());\r
+ failed = true;\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (JobExecutionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ if (failed == true) {\r
+ failedOptionPairs.add(args);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ System.out.println("failedOptionPairs: " + failedOptionPairs);\r
+ }\r
+ \r
+ /*\r
+ * This test method stolen from the other parameter testing classes\r
+ * the only purpose of the Collections.shuffle(params) and the for loop\r
+ * is to test giving the executable the parameters in different orders\r
+ * which leads to a lot of (unnecessary?) tests with an argument list\r
+ * as long as this one.\r
+ * \r
+ */\r
+ \r
+ \r
+ void test(List<? extends Option<?>> params) {\r
+ for (int i = 0; i < params.size(); i++) {\r
+ List<String> args = rnaalifoldOpc.argumentsToCommandString(params);\r
+ singleTest(args);\r
+ Collections.shuffle(params);\r
+ }\r
+ log.info("NUMBER OF COMBINATION TESTED: " + params.size());\r
+ }\r
+ \r
+ // because some parameters presuppose the -p option\r
+ \r
+ void test(List<? extends Option<?>> params, List<String> precursor) {\r
+\r
+ for (int i = 0; i < params.size(); i++) {\r
+ List<String> args = rnaalifoldOpc.argumentsToCommandString(params);\r
+ args.addAll(precursor);\r
+ singleTest(args);\r
+ Collections.shuffle(params);\r
+ }\r
+ log.info("NUMBER OF COMBINATION TESTED: " + params.size());\r
+ }\r
+ @Test\r
+ void singleParamTest() {\r
+ //List<Parameter<?>> params = rnaalifoldOpc.getAllParameters();\r
+ //System.out.println("special: params: " + params);\r
+ \r
+ //List<String> args = rnaalifoldOpc.argumentsToCommandString(params);\r
+ List<String> args = new ArrayList<String>();\r
+ //args.add("-T 37"); args.add("-S 1.07"); args.add("--stochBT_en 10");\r
+ // replace "=" with " " to fail test\r
+ args.add("--MEA=1");\r
+ args.add("-p");\r
+ singleTest(args);\r
+ \r
+ }\r
+ \r
+ void singleTest(List<String> params) {\r
+ try {\r
+ log.info("Using arguments: " + params);\r
+ RNAalifold rnaalifold = new RNAalifold();\r
+ rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput(test_outfile);\r
+ \r
+ ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator\r
+ .configureExecutable(rnaalifold, ExecProvider.Local);\r
+ // Add options to the executable\r
+ confRNAalifold.addParameters(params);\r
+ LocalRunner lr = new LocalRunner(confRNAalifold);\r
+ lr.executeJob();\r
+ confRNAalifold = (ConfiguredExecutable<RNAalifold>) lr.waitForResult();\r
+ assertNotNull(confRNAalifold.getResults(), "results is null");\r
+ \r
+ System.out.println("Results: \n" \r
+ + ((RNAStructScoreManager) confRNAalifold.getResults()).toString());\r
+ \r
+ File errors = new File(confRNAalifold.getWorkDirectory(),\r
+ ExecutableWrapper.PROC_ERR_FILE);\r
+ if (errors.length() != 0) {\r
+ log.error("PROBLEMS:\n " + FileUtil.readFileToString(errors));\r
+ }\r
+ assertTrue(errors.length() == 0, "Run with arguments : " + params\r
+ + " FAILED!");\r
+ Collections.shuffle(params);\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (JobExecutionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ }\r
+ \r
+ /* A version of singleTest that continues running instead of calling\r
+ * fail() when it encounters a problem\r
+ * \r
+ * Used to identify incompatible options and parameters\r
+ * returns -1 on failure\r
+ * \r
+ * Bad Progamming practice? \r
+ */\r
+ \r
+ \r
+ boolean singleRun(List<String> params) throws JobSubmissionException,\r
+ JobExecutionException, IOException, ResultNotAvailableException {\r
+ boolean fail = true;\r
+ log.info("Using arguments: " + params);\r
+ RNAalifold rnaalifold = new RNAalifold();\r
+ rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput(test_outfile);\r
+\r
+ ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator\r
+ .configureExecutable(rnaalifold, ExecProvider.Local);\r
+ // Add options to the executable\r
+ confRNAalifold.addParameters(params);\r
+ LocalRunner lr = new LocalRunner(confRNAalifold);\r
+ lr.executeJob();\r
+ confRNAalifold = (ConfiguredExecutable<RNAalifold>) lr.waitForResult();\r
+ \r
+ System.out.println("Results: \n" \r
+ + ((RNAStructScoreManager) confRNAalifold.getResults()).toString());\r
+ if (confRNAalifold.getResults() != null) fail = false;\r
+ File errors = new File(confRNAalifold.getWorkDirectory(),\r
+ ExecutableWrapper.PROC_ERR_FILE);\r
+ if (errors.length() != 0) {\r
+ log.error("PROBLEMS:\n " + FileUtil.readFileToString(errors));\r
+ }\r
+ assertTrue(errors.length() == 0, "Run with arguments : " + params\r
+ + " FAILED!");\r
+ Collections.shuffle(params);\r
+ return fail;\r
+ }\r
+}\r
-package compbio.runner.structure;
-
-
-import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertFalse;
-import static org.testng.Assert.assertNotNull;
-import static org.testng.Assert.assertNull;
-import static org.testng.Assert.assertTrue;
-import static org.testng.Assert.fail;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.text.ParseException;
-
-import javax.xml.bind.ValidationException;
-
-import org.apache.log4j.*;
-import org.ggf.drmaa.DrmaaException;
-import org.ggf.drmaa.JobInfo;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import compbio.data.sequence.Score;
-import compbio.data.sequence.ScoreManager;
-import compbio.data.sequence.ScoreManager.ScoreHolder;
-import compbio.data.sequence.SequenceUtil;
-import compbio.engine.AsyncExecutor;
-import compbio.engine.Configurator;
-import compbio.engine.SyncExecutor;
-import compbio.engine.client.ConfExecutable;
-import compbio.engine.client.ConfiguredExecutable;
-import compbio.engine.client.Executable;
-import compbio.engine.client.RunConfiguration;
-import compbio.engine.cluster.drmaa.ClusterUtil;
-import compbio.engine.cluster.drmaa.JobRunner;
-import compbio.engine.cluster.drmaa.StatisticManager;
-import compbio.engine.local.AsyncLocalRunner;
-import compbio.engine.local.LocalExecutorService;
-import compbio.engine.local.LocalRunner;
-import compbio.metadata.AllTestSuit;
-import compbio.metadata.JobExecutionException;
-import compbio.metadata.JobStatus;
-import compbio.metadata.JobSubmissionException;
-import compbio.metadata.LimitsManager;
-import compbio.metadata.PresetManager;
-import compbio.metadata.ResultNotAvailableException;
-import compbio.metadata.RunnerConfig;
-import compbio.runner.msa.ClustalW;
-import compbio.runner.structure.RNAalifold;
-
-public class RNAalifoldTester {
-
- private static Logger log = Logger
- .getLogger(AllTestSuit.RUNNER_TEST_LOGGER);
-
-
- private RNAalifold rnaalifold;
-
- static final String rnaalifoldConfigFile = AllTestSuit.TEST_DATA_PATH
- + "RNAalifoldParameters.xml";
- public static String test_outfile = "rnaalifold.out";
-
-
- @Test(groups = { AllTestSuit.test_group_runner })
- public void testRunLocally() {
- RNAalifold rnaalifold = new RNAalifold();
- rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput(test_outfile);
- try{
-
- ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator
- .configureExecutable(rnaalifold, Executable.ExecProvider.Local);
- LocalRunner lr = new LocalRunner(confRNAalifold);
- lr.executeJob();
- confRNAalifold = (ConfiguredExecutable<RNAalifold>) lr.waitForResult();
-
- System.out.println("TEST");
- System.out.println(((ScoreManager) confRNAalifold.getResults()).asRNAStruct().toString());
-
- assertNotNull(confRNAalifold.getResults());
- } catch (JobSubmissionException e) {
- e.printStackTrace();
- fail(e.getLocalizedMessage());
- } catch (JobExecutionException e) {
- e.printStackTrace();
- fail(e.getLocalizedMessage());
- } catch (ResultNotAvailableException e) {
- e.printStackTrace();
- fail(e.getLocalizedMessage());
- }
- }
-
-
- public static void main(String[] args) throws JobSubmissionException,
- JobExecutionException, InterruptedException, ResultNotAvailableException {
-
-
- log.warn("Logger test :- Run RNAalifold.main()");
-
- RNAalifold rnaalifold = new RNAalifold();
- rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput("test_outfile.txt");
-
- ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator
- .configureExecutable(rnaalifold);
- AsyncExecutor lr = new AsyncLocalRunner();
- lr.submitJob(confRNAalifold);
-
-
- System.out.println(((ScoreManager) confRNAalifold.getResults()).asRNAStruct().toString());
-
-
- Thread.sleep(3000);
- LocalExecutorService.shutDown();
-
- }
-
-}
+package compbio.runner.structure;\r
+\r
+\r
+import static org.testng.Assert.assertEquals;\r
+import static org.testng.Assert.assertFalse;\r
+import static org.testng.Assert.assertNotNull;\r
+import static org.testng.Assert.assertNull;\r
+import static org.testng.Assert.assertTrue;\r
+import static org.testng.Assert.fail;\r
+\r
+import java.io.File;\r
+import java.io.FileInputStream;\r
+import java.io.FileNotFoundException;\r
+import java.io.IOException;\r
+import java.text.ParseException;\r
+\r
+import javax.xml.bind.ValidationException;\r
+\r
+import org.apache.log4j.*;\r
+import org.ggf.drmaa.DrmaaException;\r
+import org.ggf.drmaa.JobInfo;\r
+import org.testng.annotations.BeforeMethod;\r
+import org.testng.annotations.Test;\r
+\r
+import compbio.data.sequence.RNAStructScoreManager;\r
+import compbio.data.sequence.Score;\r
+import compbio.data.sequence.ScoreManager;\r
+import compbio.data.sequence.ScoreManager.ScoreHolder;\r
+import compbio.data.sequence.SequenceUtil;\r
+import compbio.engine.AsyncExecutor;\r
+import compbio.engine.Configurator;\r
+import compbio.engine.SyncExecutor;\r
+import compbio.engine.client.ConfExecutable;\r
+import compbio.engine.client.ConfiguredExecutable;\r
+import compbio.engine.client.Executable;\r
+import compbio.engine.client.RunConfiguration;\r
+import compbio.engine.cluster.drmaa.ClusterUtil;\r
+import compbio.engine.cluster.drmaa.JobRunner;\r
+import compbio.engine.cluster.drmaa.StatisticManager;\r
+import compbio.engine.local.AsyncLocalRunner;\r
+import compbio.engine.local.LocalExecutorService;\r
+import compbio.engine.local.LocalRunner;\r
+import compbio.metadata.AllTestSuit;\r
+import compbio.metadata.JobExecutionException;\r
+import compbio.metadata.JobStatus;\r
+import compbio.metadata.JobSubmissionException;\r
+import compbio.metadata.LimitsManager;\r
+import compbio.metadata.PresetManager;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.metadata.RunnerConfig;\r
+import compbio.runner.msa.ClustalW;\r
+import compbio.runner.structure.RNAalifold;\r
+\r
+public class RNAalifoldTester {\r
+\r
+ private static Logger log = Logger\r
+ .getLogger(AllTestSuit.RUNNER_TEST_LOGGER);\r
+ \r
+ \r
+ private RNAalifold rnaalifold;\r
+ \r
+ static final String rnaalifoldConfigFile = AllTestSuit.TEST_DATA_PATH\r
+ + "RNAalifoldParameters.xml";\r
+ public static String test_outfile = "rnaalifold.out";\r
+ \r
+ \r
+ @Test(groups = { AllTestSuit.test_group_runner })\r
+ public void testRunLocally() {\r
+ RNAalifold rnaalifold = new RNAalifold();\r
+ rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput(test_outfile);\r
+ try{\r
+ \r
+ ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator\r
+ .configureExecutable(rnaalifold, Executable.ExecProvider.Local);\r
+ LocalRunner lr = new LocalRunner(confRNAalifold);\r
+ lr.executeJob();\r
+ confRNAalifold = (ConfiguredExecutable<RNAalifold>) lr.waitForResult();\r
+ \r
+ System.out.println("TEST");\r
+ System.out.println(((RNAStructScoreManager) confRNAalifold.getResults()).toString());\r
+ \r
+ assertNotNull(confRNAalifold.getResults()); \r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (JobExecutionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ }\r
+ \r
+ \r
+ public static void main(String[] args) throws JobSubmissionException,\r
+ JobExecutionException, InterruptedException, ResultNotAvailableException {\r
+\r
+ \r
+ log.warn("Logger test :- Run RNAalifold.main()");\r
+\r
+ RNAalifold rnaalifold = new RNAalifold();\r
+ rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput("test_outfile.txt");\r
+ \r
+ ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator\r
+ .configureExecutable(rnaalifold);\r
+ AsyncExecutor lr = new AsyncLocalRunner();\r
+ lr.submitJob(confRNAalifold);\r
+ \r
+ \r
+ System.out.println(((RNAStructScoreManager) confRNAalifold.getResults()).toString());\r
+\r
+ \r
+ Thread.sleep(3000);\r
+ LocalExecutorService.shutDown();\r
+ \r
+ }\r
+ \r
+}\r
- package compbio.ws.client;
-
-import compbio.metadata.AllTestSuit;
-import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertNotNull;
-import static org.testng.Assert.fail;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.net.ConnectException;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.xml.ws.WebServiceException;
-
-import org.testng.annotations.BeforeTest;
-import org.testng.annotations.Test;
-
-import compbio.data.msa.FoldWS;
-import compbio.data.msa.JABAService;
-import compbio.data.msa.SequenceAnnotation;
-import compbio.data.sequence.Alignment;
-import compbio.data.sequence.RNAStruct;
-import compbio.data.sequence.ClustalAlignmentUtil;
-import compbio.data.sequence.ConservationMethod;
-import compbio.data.sequence.FastaSequence;
-import compbio.data.sequence.ScoreManager;
-import compbio.data.sequence.SequenceUtil;
-import compbio.data.sequence.UnknownFileFormatException;
-import compbio.metadata.AllTestSuit;
-import compbio.metadata.JobSubmissionException;
-import compbio.metadata.LimitExceededException;
-import compbio.metadata.Option;
-import compbio.metadata.PresetManager;
-import compbio.metadata.ResultNotAvailableException;
-import compbio.metadata.RunnerConfig;
-import compbio.metadata.UnsupportedRuntimeException;
-import compbio.metadata.WrongParameterException;
-import compbio.runner.conservation.AACon;
-import compbio.util.SysPrefs;
-import compbio.ws.server.RNAalifoldWS;
-
-
-public class TestRNAalifoldWS {
-
- SequenceAnnotation<RNAalifoldWS> foldws;
-
- @BeforeTest(groups = {AllTestSuit.test_group_webservices})
- void initConnection() {
-
- try {
- JABAService client = Jws2Client.connect(
- "http://localhost:8080/jabaws", Services.RNAalifoldWS);
- foldws = (SequenceAnnotation<RNAalifoldWS>) client;
- } catch (ConnectException e) {
- e.printStackTrace();
- fail(e.getMessage());
- } catch (WebServiceException e) {
- e.printStackTrace();
- fail(e.getMessage());
- }
- }
-
-
- @Test(groups = {AllTestSuit.test_group_webservices})
- public void testFold() throws FileNotFoundException, IOException,
- UnknownFileFormatException {
-
-// String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
-// + File.separator;
-
- Alignment aln = ClustalAlignmentUtil.readClustalFile(new FileInputStream(
- AllTestSuit.test_input_aln));
-
- List<FastaSequence> fsl = aln.getSequences();
-
- try {
- List<Option<RNAalifoldWS>> options = new ArrayList<Option<RNAalifoldWS>>();
- options.add(foldws.getRunnerOptions().getArgumentByOptionName("--mis"));
- options.add(foldws.getRunnerOptions().getArgumentByOptionName("-p"));
- options.add(foldws.getRunnerOptions().getArgumentByOptionName("--MEA"));
-
- System.out.println("TestRNAalifoldWS: print options: " + options.toString());
-
- String jobId = foldws.customAnalize(fsl, options);
- System.out.println("J: " + jobId);
- ScoreManager result = foldws.getAnnotation(jobId);
- System.out.println("fold results: \n" + result.asRNAStruct().toString());
- assertNotNull(result);
-
- } catch (UnsupportedRuntimeException e) {
- e.printStackTrace();
- fail(e.getMessage());
- } catch (LimitExceededException e) {
- e.printStackTrace();
- fail(e.getMessage());
- } catch (JobSubmissionException e) {
- e.printStackTrace();
- fail(e.getMessage());
- } catch (ResultNotAvailableException e) {
- e.printStackTrace();
- fail(e.getMessage());
- } catch (WrongParameterException e) {
- e.printStackTrace();
- fail(e.getMessage());
- }
- }
-}
-
-
-
+ package compbio.ws.client;\r
+\r
+import static org.testng.Assert.assertNotNull;\r
+import static org.testng.Assert.fail;\r
+\r
+import java.io.FileInputStream;\r
+import java.io.FileNotFoundException;\r
+import java.io.IOException;\r
+import java.io.OutputStreamWriter;\r
+import java.io.Writer;\r
+import java.net.ConnectException;\r
+import java.util.ArrayList;\r
+import java.util.List;\r
+\r
+import javax.xml.ws.WebServiceException;\r
+\r
+import org.testng.annotations.BeforeTest;\r
+import org.testng.annotations.Test;\r
+\r
+import compbio.data.msa.JABAService;\r
+import compbio.data.msa.SequenceAnnotation;\r
+import compbio.data.sequence.Alignment;\r
+import compbio.data.sequence.ClustalAlignmentUtil;\r
+import compbio.data.sequence.FastaSequence;\r
+import compbio.data.sequence.RNAStructScoreManager;\r
+import compbio.data.sequence.ScoreManager;\r
+import compbio.data.sequence.UnknownFileFormatException;\r
+import compbio.metadata.AllTestSuit;\r
+import compbio.metadata.JobSubmissionException;\r
+import compbio.metadata.LimitExceededException;\r
+import compbio.metadata.Option;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.metadata.UnsupportedRuntimeException;\r
+import compbio.metadata.WrongParameterException;\r
+import compbio.runner.structure.RNAalifold;\r
+import compbio.ws.server.RNAalifoldWS;\r
+\r
+\r
+public class TestRNAalifoldWS {\r
+ \r
+// SequenceAnnotation<RNAalifoldWS> foldws;\r
+ RNAalifoldWS foldws;\r
+ \r
+ @BeforeTest(groups = {AllTestSuit.test_group_webservices})\r
+ void initConnection() {\r
+ \r
+ try {\r
+ JABAService client = Jws2Client.connect(\r
+ "http://localhost:8080/jabaws", Services.RNAalifoldWS);\r
+ foldws = (RNAalifoldWS) client;\r
+ } catch (ConnectException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (WebServiceException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+ }\r
+\r
+ \r
+ @Test(groups = {AllTestSuit.test_group_webservices})\r
+ public void testFold() throws FileNotFoundException, IOException,\r
+ UnknownFileFormatException {\r
+ \r
+// String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()\r
+// + File.separator;\r
+ \r
+ Alignment aln = ClustalAlignmentUtil.readClustalFile(new FileInputStream(\r
+ AllTestSuit.test_input_aln));\r
+ \r
+ List<FastaSequence> fsl = aln.getSequences();\r
+ \r
+ try {\r
+ List<Option<RNAalifold>> options = new ArrayList<Option<RNAalifold>>();\r
+ options.add(foldws.getRunnerOptions().getArgumentByOptionName("--mis"));\r
+ options.add(foldws.getRunnerOptions().getArgumentByOptionName("-p"));\r
+ options.add(foldws.getRunnerOptions().getArgumentByOptionName("--MEA"));\r
+ \r
+// System.out.println("TestRNAalifoldWS: print options: " + options.toString());\r
+ \r
+ String jobId = foldws.customAnalize(fsl, options);\r
+ System.out.println("J: " + jobId);\r
+ \r
+ Writer stdout = new OutputStreamWriter(System.out);\r
+ \r
+ System.out.println("results class: " + foldws.getAnnotation(jobId).getClass().getName());\r
+ RNAStructScoreManager result = (RNAStructScoreManager)foldws.getAnnotation(jobId);\r
+ \r
+ \r
+ result.writeOut(stdout);\r
+ System.out.println("fold results: \n" + result.toString());\r
+ assertNotNull(result);\r
+ \r
+ } catch (UnsupportedRuntimeException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (LimitExceededException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (WrongParameterException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+ }\r
+}\r
+ \r
+\r
+\r
-package compbio.ws.server;
-
-import java.io.File;
-import java.util.List;
-
-import javax.jws.WebParam;
-import javax.jws.WebService;
-
-import org.apache.log4j.Logger;
-
-import compbio.data.msa.FoldWS;
-import compbio.data.msa.JABAService;
-import compbio.data.msa.JManagement;
-import compbio.data.msa.Metadata;
-import compbio.data.msa.SequenceAnnotation;
-import compbio.data.sequence.Alignment;
-import compbio.data.sequence.RNAStruct;
-import compbio.data.sequence.FastaSequence;
-import compbio.engine.AsyncExecutor;
-import compbio.engine.Configurator;
-import compbio.engine.client.ConfiguredExecutable;
-import compbio.engine.client.SkeletalExecutable;
-import compbio.metadata.ChunkHolder;
-import compbio.metadata.JobStatus;
-import compbio.metadata.JobSubmissionException;
-import compbio.metadata.Limit;
-import compbio.metadata.LimitExceededException;
-import compbio.metadata.LimitsManager;
-import compbio.metadata.Option;
-import compbio.metadata.Preset;
-import compbio.metadata.PresetManager;
-import compbio.metadata.ResultNotAvailableException;
-import compbio.metadata.RunnerConfig;
-import compbio.metadata.UnsupportedRuntimeException;
-import compbio.metadata.WrongParameterException;
-import compbio.runner.Util;
-import compbio.runner.disorder.GlobPlot;
-import compbio.runner.structure.RNAalifold;
-
-@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "RNAalifoldWS")
-public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold>
- implements
- SequenceAnnotation<RNAalifold> {
-
- private static Logger log = Logger.getLogger(ClustalWS.class);
-
- public RNAalifoldWS() {
- super (new RNAalifold(), log);
- }
-
-
- /*
- * No presets are supported, thus the result of this call will be as simple
- * call to analize without parameters
- */
- @Override
- public String presetAnalize(List<FastaSequence> sequences,
- Preset<RNAalifold> preset) throws UnsupportedRuntimeException,
- LimitExceededException, JobSubmissionException,
- WrongParameterException {
-
- return analize(sequences);
- }
-}
-
-
+package compbio.ws.server;\r
+\r
+import java.util.List;\r
+\r
+import javax.jws.WebService;\r
+\r
+import org.apache.log4j.Logger;\r
+\r
+import compbio.data.msa.JABAService;\r
+import compbio.data.msa.SequenceAnnotation;\r
+import compbio.data.sequence.FastaSequence;\r
+import compbio.data.sequence.RNAStructScoreManager;\r
+import compbio.engine.client.ConfiguredExecutable;\r
+import compbio.metadata.JobSubmissionException;\r
+import compbio.metadata.LimitExceededException;\r
+import compbio.metadata.Option;\r
+import compbio.metadata.Preset;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.metadata.UnsupportedRuntimeException;\r
+import compbio.metadata.WrongParameterException;\r
+import compbio.runner.conservation.AACon;\r
+import compbio.runner.structure.RNAalifold;\r
+\r
+@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "RNAalifoldWS")\r
+public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold> \r
+ implements\r
+ SequenceAnnotation<RNAalifold> {\r
+\r
+ private static Logger log = Logger.getLogger(RNAalifoldWS.class);\r
+ \r
+ public RNAalifoldWS() {\r
+ super (new RNAalifold(), log);\r
+ }\r
+\r
+ \r
+ // for testing\r
+ @Override\r
+ public RNAStructScoreManager getAnnotation(String jobId) \r
+ throws ResultNotAvailableException {\r
+ return WSUtil.getAnnotation(jobId, log);\r
+ }\r
+ \r
+ @Override\r
+ public String analize(List<FastaSequence> sequences)\r
+ throws UnsupportedRuntimeException, LimitExceededException,\r
+ JobSubmissionException {\r
+ WSUtil.validateFastaInput(sequences);\r
+ ConfiguredExecutable<RNAalifoldWS> confRNAalifold = init(sequences);\r
+ return WSUtil.fold(sequences, confRNAalifold, log, "analize",\r
+ getLimit(""));\r
+ }\r
+\r
+ @Override\r
+ public String customAnalize(List<FastaSequence> sequences,\r
+ List<Option<RNAalifold>> options) throws UnsupportedRuntimeException,\r
+ LimitExceededException, JobSubmissionException,\r
+ WrongParameterException {\r
+ WSUtil.validateFastaInput(sequences);\r
+ ConfiguredExecutable<RNAalifold> confRNAalifold = init(sequences);\r
+ \r
+ List<String> params = WSUtil.getCommands(options,\r
+ AACon.KEY_VALUE_SEPARATOR);\r
+ confRNAalifold.addParameters(params);\r
+ return WSUtil.fold(sequences, confRNAalifold, log, "customAnalize",\r
+ getLimit(""));\r
+ }\r
+ \r
+ \r
+ /*\r
+ * No presets are supported, thus the result of this call will be as simple\r
+ * call to analize without parameters\r
+ */\r
+ @Override\r
+ public String presetAnalize(List<FastaSequence> sequences,\r
+ Preset<RNAalifold> preset) throws UnsupportedRuntimeException,\r
+ LimitExceededException, JobSubmissionException,\r
+ WrongParameterException {\r
+\r
+ return analize(sequences);\r
+ }\r
+}\r
+ \r
+ \r
git://source.jalview.org / jabaws.git / commitdiff