GlobPlot service, runner and result parser

Some rearrangements for disembl to reuse methods

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3709 e3abac25-378b-4346-85de-24260fe3988d

diff --git a/binaries/src/disembl/DisEMBL.py b/binaries/src/disembl/DisEMBL.py
index d9618e2..7298e83 100644 (file)
--- a/binaries/src/disembl/DisEMBL.py
+++ b/binaries/src/disembl/DisEMBL.py
@@ -118,13 +118,8 @@ def reportSlicesTXT(slices, sequence):
             if i > 0:
                 sys.stdout.write(', ')
             sys.stdout.write( str(slices[i][0]+1) + '-' + str(slices[i][1]+1) )
-            s = s + upper(sequence[slices[i][0]:(slices[i][1]+1)])
-            if i < len(slices)-1:
-                s = s + lower(sequence[(slices[i][1]+1):(slices[i+1][0])])
-            elif slices[i][1] < len(sequence)-1:
-                s = s + lower(sequence[(slices[i][1]+1):(len(sequence))])
+           
     print ''
-    print s
 
 
 
@@ -144,7 +139,6 @@ def runDisEMBLpipeline():
     except:
         print '\nDisEMBL.py sequence_file \n'
         print 'A default run would be: ./DisEMBL.py fasta_file'
-        print 'Mode: "default"(nothing) or "scores" which will give scores per residue in TAB seperated format'
         raise SystemExit
     #db = sys.stdin
     parser = Fasta.RecordParser()
@@ -159,22 +153,17 @@ def runDisEMBLpipeline():
             REM465_smooth = SavitzkyGolay(smooth_frame,0,REM465_raw)
             COILS_smooth = SavitzkyGolay(smooth_frame,0,COILS_raw)
             HOTLOOPS_smooth = SavitzkyGolay(smooth_frame,0,HOTLOOPS_raw)
-            if mode == 'default':
-                sys.stdout.write('> '+cur_record.title+'_COILS ')
-                reportSlicesTXT( getSlices(COILS_smooth, fold_coils, join_frame, peak_frame, 0.43), sequence )
-                sys.stdout.write('> '+cur_record.title+'_REM465 ')
-                reportSlicesTXT( getSlices(REM465_smooth, fold_rem465, join_frame, peak_frame, 0.50), sequence )
-                sys.stdout.write('> '+cur_record.title+'_HOTLOOPS ')
-                reportSlicesTXT( getSlices(HOTLOOPS_smooth, fold_hotloops, join_frame, peak_frame, 0.086), sequence )
-                sys.stdout.write('\n')
-            elif mode == 'scores':
-                sys.stdout.write('> '+cur_record.title+'\n')
-                sys.stdout.write('# RESIDUE COILS REM465 HOTLOOPS\n')
-                for i in range(len(REM465_smooth)):
-                    sys.stdout.write(sequence[i]+'\t'+fpformat.fix(COILS_smooth[i],5)+'\t'+fpformat.fix(REM465_smooth[i],5)+'\t'+fpformat.fix(HOTLOOPS_smooth[i],5)+'\n')
-            else:
-                sys.stderr.write('Wrong mode given: '+mode+'\n')
-                raise SystemExit
+
+            sys.stdout.write('> '+cur_record.title+'\n')
+            sys.stdout.write('# COILS ')
+            reportSlicesTXT( getSlices(COILS_smooth, fold_coils, join_frame, peak_frame, 0.43), sequence )
+            sys.stdout.write('# REM465 ')
+            reportSlicesTXT( getSlices(REM465_smooth, fold_rem465, join_frame, peak_frame, 0.50), sequence )
+            sys.stdout.write('# HOTLOOPS ')
+            reportSlicesTXT( getSlices(HOTLOOPS_smooth, fold_hotloops, join_frame, peak_frame, 0.086), sequence )
+            sys.stdout.write('# RESIDUE COILS REM465 HOTLOOPS\n')
+            for i in range(len(REM465_smooth)):
+                sys.stdout.write(sequence[i]+'\t'+fpformat.fix(COILS_smooth[i],5)+'\t'+fpformat.fix(REM465_smooth[i],5)+'\t'+fpformat.fix(HOTLOOPS_smooth[i],5)+'\n')
         except AttributeError:
             break
     file.close()

diff --git a/binaries/src/globplot/GlobPipe.py b/binaries/src/globplot/GlobPipe.py
index 71be8a7..b15a28d 100644 (file)
--- a/binaries/src/globplot/GlobPipe.py
+++ b/binaries/src/globplot/GlobPipe.py
@@ -123,9 +123,9 @@ def SavitzkyGolay(window,derivative,datalist):
 
 def reportSlicesTXT(slices, sequence, maskFlag):
     if maskFlag == 'DOM':
-        coordstr = '|GlobDoms:'
+        coordstr = 'GlobDoms '
     elif maskFlag == 'DIS':
-        coordstr = '|Disorder:'
+        coordstr = 'Disorder '
     else:
         raise SystemExit
     if slices == []:
@@ -163,18 +163,16 @@ def reportSlicesTXT(slices, sequence, maskFlag):
 
 def runGlobPlot():
     try:
-        smoothFrame = int(sys.argv[1])
-        DOM_joinFrame = int(sys.argv[2])
-        DOM_peakFrame = int(sys.argv[3])
-        DIS_joinFrame = int(sys.argv[4])
-        DIS_peakFrame = int(sys.argv[5])
-        file = str(sys.argv[6])
+        smoothFrame = 10
+        DOM_joinFrame = 15
+        DOM_peakFrame = 74
+        DIS_joinFrame = 4
+        DIS_peakFrame = 5
+        file = str(sys.argv[1])
         db = open(file,'r')
     except:
         print 'Usage:'
-        print '         ./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame FASTAfile'
-        print '         Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file'
-        print '         Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file'
+        print '         ./GlobPipe.py FASTAfile'
         raise SystemExit
     parser = Fasta.RecordParser()
     iterator = Fasta.Iterator(db,parser)
@@ -209,9 +207,12 @@ def runGlobPlot():
             globdoms, globdis = getSlices(dydx_vector, DOM_joinFrame, DOM_peakFrame, DIS_joinFrame, DIS_peakFrame)
             s_domMask, coordstrDOM = reportSlicesTXT(globdoms, seq, 'DOM')
             s_final, coordstrDIS = reportSlicesTXT(globdis, s_domMask, 'DIS')
-            sys.stdout.write('>'+cur_record.title+coordstrDOM+coordstrDIS+'\n')
+            sys.stdout.write('>'+cur_record.title+'\n')
+            sys.stdout.write('# '+coordstrDOM+'\n')
+            sys.stdout.write('# '+coordstrDIS+'\n')
 
 # UNCOMMENT THIS IF NEED TO PRODUCE PER RESEDUE VALUES 
+            sys.stdout.write('# RESIDUE' + '\t' + 'DYDX' + '\t' + 'RAW' + '\t' +'SMOOTHED\n')
             for i in range(len(dydx_vector)):
 # dydx (positive values seems to indicate disorder in rows more than ~6 chars)  raw    smoothed
                sys.stdout.write(seq[i]+'\t'+fpformat.fix(dydx_vector[i],4)+ '\t'+fpformat.fix(smooth[i],4)+'\t'+fpformat.fix(sum_vector[i],4)+ '\n')

diff --git a/datamodel/compbio/data/sequence/DisemblResultAnnot.java b/datamodel/compbio/data/sequence/DisemblResultAnnot.java
deleted file mode 100644 (file)
index c5f026c..0000000
--- a/datamodel/compbio/data/sequence/DisemblResultAnnot.java
+++ /dev/null
@@ -1,5 +0,0 @@
-package compbio.data.sequence;\r
-\r
-public enum DisemblResultAnnot {\r
-       COILS, REM465, HOTLOOPS\r
-}\r

diff --git a/datamodel/compbio/data/sequence/Range.java b/datamodel/compbio/data/sequence/Range.java
new file mode 100644 (file)
index 0000000..839ae28
--- /dev/null
+++ b/datamodel/compbio/data/sequence/Range.java
@@ -0,0 +1,57 @@
+package compbio.data.sequence;\r
+\r
+public class Range implements Comparable<Range> {\r
+\r
+       public final int from;\r
+       public final int to;\r
+\r
+       public Range(int from, int to) {\r
+               this.from = from;\r
+               this.to = to;\r
+       }\r
+\r
+       public Range(String[] twoElementAr) {\r
+               if (twoElementAr == null || twoElementAr.length != 2) {\r
+                       throw new IllegalArgumentException();\r
+               }\r
+               this.from = Integer.parseInt(twoElementAr[0].trim());\r
+               this.to = Integer.parseInt(twoElementAr[1].trim());\r
+       }\r
+\r
+       @Override\r
+       public String toString() {\r
+               return "[" + from + ", " + to + "]";\r
+       }\r
+\r
+       @Override\r
+       public int hashCode() {\r
+               final int prime = 31;\r
+               int result = 1;\r
+               result = prime * result + from;\r
+               result = prime * result + to;\r
+               return result;\r
+       }\r
+       @Override\r
+       public boolean equals(Object obj) {\r
+               if (this == obj)\r
+                       return true;\r
+               if (obj == null)\r
+                       return false;\r
+               if (getClass() != obj.getClass())\r
+                       return false;\r
+               Range other = (Range) obj;\r
+               if (from != other.from)\r
+                       return false;\r
+               if (to != other.to)\r
+                       return false;\r
+               return true;\r
+       }\r
+\r
+       @Override\r
+       public int compareTo(Range o) {\r
+               if (o == null)\r
+                       return 1;\r
+               return new Integer(this.from).compareTo(new Integer(o.from));\r
+       }\r
+\r
+}\r

diff --git a/datamodel/compbio/data/sequence/Score.java b/datamodel/compbio/data/sequence/Score.java
index 8a110ee..39bb398 100644 (file)
--- a/datamodel/compbio/data/sequence/Score.java
+++ b/datamodel/compbio/data/sequence/Score.java
@@ -6,10 +6,12 @@ import java.io.OutputStream;
 import java.io.OutputStreamWriter;\r
 import java.text.NumberFormat;\r
 import java.util.ArrayList;\r
-import java.util.Arrays;\r
+import java.util.Collections;\r
 import java.util.List;\r
 import java.util.Locale;\r
 import java.util.Set;\r
+import java.util.SortedSet;\r
+import java.util.TreeSet;\r
 \r
 import javax.xml.bind.annotation.XmlAccessType;\r
 import javax.xml.bind.annotation.XmlAccessorType;\r
@@ -36,7 +38,9 @@ public class Score {
 \r
        private Enum<?> method;\r
 \r
-       private List<Float> scores;\r
+       private SortedSet<Range> ranges = new TreeSet<Range>();\r
+\r
+       private List<Float> scores = Collections.emptyList();\r
 \r
        private Score() {\r
                // JaXB default constructor\r
@@ -57,6 +61,28 @@ public class Score {
                this.scores = new ArrayList<Float>(scores);\r
        }\r
 \r
+       /**\r
+        * @param method\r
+        *            the ConservationMethod with which {@code scores} were\r
+        *            calculated\r
+        * @param scores\r
+        *            the actual conservation values for each column of the\r
+        *            alignment\r
+        * @param ranges\r
+        *            The set of ranges i.e. parts of the sequence with specific\r
+        *            function, usually can be calculated based on scores\r
+        */\r
+       public Score(Enum<?> method, List<Float> scores, SortedSet<Range> ranges) {\r
+               this.method = method;\r
+               this.ranges = ranges;\r
+               this.scores = scores;\r
+       }\r
+\r
+       public Score(Enum<?> method, SortedSet<Range> ranges) {\r
+               this.method = method;\r
+               this.ranges = ranges;\r
+       }\r
+\r
        public Score(Enum<?> method, float[] scores) {\r
                this.method = method;\r
                this.scores = toList(scores);\r
@@ -87,25 +113,35 @@ public class Score {
                return scores;\r
        }\r
 \r
+       /**\r
+        * Return Ranges if any Collections.EMPTY_SET otherwise\r
+        * \r
+        * @return\r
+        */\r
+       public SortedSet<Range> getRanges() {\r
+               return ranges;\r
+       }\r
+\r
+       public void setRanges(SortedSet<Range> ranges) {\r
+               this.ranges = ranges;\r
+       }\r
+\r
        @Override\r
        public String toString() {\r
-               return "Score [method=" + method + ", scores=" + scores + "]";\r
+               return "Score [method=" + method + ", ranges=" + ranges + ", scores="\r
+                               + scores + "]";\r
        }\r
 \r
        @Override\r
        public int hashCode() {\r
-               final int prime = 31;\r
+               final int prime = 7;\r
                int result = 1;\r
                result = prime * result + ((method == null) ? 0 : method.hashCode());\r
+               result = prime * result + ((ranges == null) ? 0 : ranges.hashCode());\r
                result = prime * result + ((scores == null) ? 0 : scores.hashCode());\r
                return result;\r
        }\r
 \r
-       /*\r
-        * TODO test ! (non-Javadoc)\r
-        * \r
-        * @see java.lang.Object#equals(java.lang.Object)\r
-        */\r
        @Override\r
        public boolean equals(Object obj) {\r
                if (this == obj)\r
@@ -115,15 +151,20 @@ public class Score {
                if (getClass() != obj.getClass())\r
                        return false;\r
                Score other = (Score) obj;\r
-               if (method != other.method)\r
+               if (method == null) {\r
+                       if (other.method != null)\r
+                               return false;\r
+               } else if (!method.equals(other.method))\r
                        return false;\r
-               if (scores == other.scores) {\r
-                       return true;\r
-               }\r
-               if (scores == null) {\r
+               if (ranges == null) {\r
+                       if (other.ranges != null)\r
+                               return false;\r
+               } else if (!ranges.equals(other.ranges))\r
                        return false;\r
-               }\r
-               if (!Arrays.deepEquals(scores.toArray(), other.scores.toArray()))\r
+               if (scores == null) {\r
+                       if (other.scores != null)\r
+                               return false;\r
+               } else if (!scores.equals(other.scores))\r
                        return false;\r
                return true;\r
        }\r

diff --git a/datamodel/compbio/data/sequence/SequenceUtil.java b/datamodel/compbio/data/sequence/SequenceUtil.java
index a636c3a..7e6c672 100644 (file)
--- a/datamodel/compbio/data/sequence/SequenceUtil.java
+++ b/datamodel/compbio/data/sequence/SequenceUtil.java
@@ -31,10 +31,14 @@ import java.util.List;
 import java.util.Map;\r
 import java.util.Scanner;\r
 import java.util.Set;\r
+import java.util.SortedSet;\r
+import java.util.TreeSet;\r
 import java.util.logging.Level;\r
 import java.util.regex.Matcher;\r
 import java.util.regex.Pattern;\r
 \r
+import compbio.util.Util;\r
+\r
 /**\r
  * Utility class for operations on sequences\r
  * \r
@@ -404,35 +408,37 @@ public final class SequenceUtil {
 \r
        /**\r
         * \r
-        * TODO complete!\r
+        > Foobar_dundeefriends\r
         * \r
-        * >Sequence name\r
+        * # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343\r
         * \r
-        * RESIDUE COILS REM465 HOTLOOPS\r
+        * # REM465 355-368\r
         * \r
-        * M 0.86010 0.88512 0.37094\r
+        * # HOTLOOPS 190-204\r
         * \r
-        * T 0.79983 0.85864 0.44331 ....\r
-\r
-        * >Next Sequence name \r
-        * RESIDUE COILS REM465 HOTLOOPS\r
+        * # RESIDUE COILS REM465 HOTLOOPS\r
         * \r
         * M 0.86010 0.88512 0.37094\r
         * \r
+        * T 0.79983 0.85864 0.44331\r
+        * \r
+        * >Next Sequence name\r
+        * \r
         * \r
         * @param input\r
         * @return\r
         * @throws IOException\r
         * @throws UnknownFileFormatException\r
         */\r
-       public static Map<FastaSequence, Set<Score>> readDisembl(final InputStream input)\r
-                       throws IOException, UnknownFileFormatException {\r
+       public static Map<FastaSequence, Set<Score>> readDisembl(\r
+                       final InputStream input) throws IOException,\r
+                       UnknownFileFormatException {\r
                Scanner scan = new Scanner(input);\r
                scan.useDelimiter(">");\r
                if (!scan.hasNext()) {\r
                        throw new UnknownFileFormatException(\r
-                                       "In Disembl score format each sequence score is expected " +\r
-                                       "to start from the line: >Sequence name "\r
+                                       "In Disembl score format each sequence score is expected "\r
+                                                       + "to start from the line: >Sequence name "\r
                                                        + " No such line was found!");\r
                }\r
 \r
@@ -441,31 +447,40 @@ public final class SequenceUtil {
                while (scan.hasNext()) {\r
                        seqCounter++;\r
                        String singleSeq = scan.next();\r
-                       Scanner scansingle = new Scanner(singleSeq);\r
-                       if(!scansingle.hasNextLine()) {\r
-                               throw new RuntimeException("The input looks like an incomplete disembl file - cannot parse!");\r
-                       }\r
-                       \r
+                       Scanner scansingle = new Scanner(singleSeq);\r
+                       if (!scansingle.hasNextLine()) {\r
+                               throw new RuntimeException(\r
+                                               "The input looks like an incomplete disembl file - cannot parse!");\r
+                       }\r
+\r
                        StringBuffer seqbuffer = new StringBuffer();\r
                        ArrayList<Float> coils = new ArrayList<Float>();\r
                        ArrayList<Float> rem = new ArrayList<Float>();\r
                        ArrayList<Float> hotloops = new ArrayList<Float>();\r
 \r
                        String sequenceName = scansingle.nextLine().trim();\r
-                       String title =  scansingle.nextLine();\r
+                       SortedSet<Range> coilsR = parseRanges(DisemblResult.COILS,\r
+                                       scansingle.nextLine());\r
+                       SortedSet<Range> rem465R = parseRanges(DisemblResult.REM465,\r
+                                       scansingle.nextLine());\r
+                       SortedSet<Range> loopsR = parseRanges(DisemblResult.HOTLOOPS,\r
+                                       scansingle.nextLine());\r
+\r
+                       String title = scansingle.nextLine();\r
                        assert title.startsWith("# RESIDUE COILS REM465 HOTLOOPS") : ">Sequence_name must follow column title: # RESIDUE COILS REM465 HOTLOOPS!";\r
-                       \r
+\r
                        while (scansingle.hasNext()) {\r
                                seqbuffer.append(scansingle.next());\r
                                coils.add(scansingle.nextFloat());\r
                                rem.add(scansingle.nextFloat());\r
                                hotloops.add(scansingle.nextFloat());\r
                        }\r
-                       FastaSequence fs = new FastaSequence(sequenceName,seqbuffer.toString());\r
+                       FastaSequence fs = new FastaSequence(sequenceName,\r
+                                       seqbuffer.toString());\r
                        Set<Score> scores = new HashSet<Score>();\r
-                       scores.add(new Score(DisemblResultAnnot.COILS, coils));\r
-                       scores.add(new Score(DisemblResultAnnot.HOTLOOPS, hotloops));\r
-                       scores.add(new Score(DisemblResultAnnot.REM465, rem));\r
+                       scores.add(new Score(DisemblResult.COILS, coils, coilsR));\r
+                       scores.add(new Score(DisemblResult.HOTLOOPS, hotloops, rem465R));\r
+                       scores.add(new Score(DisemblResult.REM465, rem, loopsR));\r
                        results.put(fs, scores);\r
 \r
                        scansingle.close();\r
@@ -474,15 +489,134 @@ public final class SequenceUtil {
                input.close();\r
                return results;\r
        }\r
-       \r
-       public static  Map<String, Set<Score>> removeSequences(Map<FastaSequence, Set<Score>> disemblResults) { \r
+\r
+       /**\r
+        * Parsing:\r
+        * \r
+        * # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343,\r
+        * 350-391, 429-485, 497-506, 539-547\r
+        * \r
+        * # REM465 355-368\r
+        * \r
+        * # HOTLOOPS 190-204\r
+        * \r
+        * @param lines\r
+        * @return\r
+        */\r
+       private static SortedSet<Range> parseRanges(Enum resultType, String lines) {\r
+               SortedSet<Range> ranges = new TreeSet<Range>();\r
+               Scanner scan = new Scanner(lines);\r
+\r
+               assert scan.hasNext();\r
+               assert "#".equals(scan.next()); // pass delimiter #\r
+               String type = scan.next(); // pass enum name e.g. COILS\r
+               assert resultType.toString().equalsIgnoreCase(type) : "Unknown result type: "\r
+                               + resultType.toString();\r
+\r
+               // beginning of the ranges\r
+               scan.useDelimiter(",");\r
+               while (scan.hasNext()) {\r
+                       String range = scan.next();\r
+                       if (!Util.isEmpty(range)) {\r
+                               ranges.add(new Range(range.split("-")));\r
+                       }\r
+               }\r
+               return ranges;\r
+       }\r
+\r
+       public static Map<String, Set<Score>> removeSequences(\r
+                       Map<FastaSequence, Set<Score>> disemblResults) {\r
                Map<String, Set<Score>> seqNameScores = new HashMap<String, Set<Score>>();\r
-               for(Map.Entry<FastaSequence,Set<Score>> dres: disemblResults.entrySet()) {\r
-                       seqNameScores.put(dres.getKey().getId(),dres.getValue()); \r
+               for (Map.Entry<FastaSequence, Set<Score>> dres : disemblResults\r
+                               .entrySet()) {\r
+                       seqNameScores.put(dres.getKey().getId(), dres.getValue());\r
                }\r
                return seqNameScores;\r
        }\r
-       \r
+\r
+       /**\r
+        * \r
+        > Foobar_dundeefriends\r
+        * \r
+        * # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343\r
+        * \r
+        * # REM465 355-368\r
+        * \r
+        * # HOTLOOPS 190-204\r
+        * \r
+        * # RESIDUE COILS REM465 HOTLOOPS\r
+        * \r
+        * M 0.86010 0.88512 0.37094\r
+        * \r
+        * T 0.79983 0.85864 0.44331\r
+        * \r
+        * >Next Sequence name\r
+        * \r
+        * \r
+        * @param input\r
+        * @return\r
+        * @throws IOException\r
+        * @throws UnknownFileFormatException\r
+        */\r
+       public static Map<FastaSequence, Set<Score>> readGlobPlot(\r
+                       final InputStream input) throws IOException,\r
+                       UnknownFileFormatException {\r
+               Scanner scan = new Scanner(input);\r
+               scan.useDelimiter(">");\r
+               if (!scan.hasNext()) {\r
+                       throw new UnknownFileFormatException(\r
+                                       "In GlobPlot score format each sequence score is expected "\r
+                                                       + "to start from the line: >Sequence name "\r
+                                                       + " No such line was found!");\r
+               }\r
+\r
+               Map<FastaSequence, Set<Score>> results = new HashMap<FastaSequence, Set<Score>>();\r
+               int seqCounter = 0;\r
+               while (scan.hasNext()) {\r
+                       seqCounter++;\r
+                       String singleSeq = scan.next();\r
+                       Scanner scansingle = new Scanner(singleSeq);\r
+                       if (!scansingle.hasNextLine()) {\r
+                               throw new RuntimeException(\r
+                                               "The input looks like an incomplete GlobPlot file - cannot parse!");\r
+                       }\r
+\r
+                       StringBuffer seqbuffer = new StringBuffer();\r
+                       ArrayList<Float> dydxScore = new ArrayList<Float>();\r
+                       ArrayList<Float> rawScore = new ArrayList<Float>();\r
+                       ArrayList<Float> smoothedScore = new ArrayList<Float>();\r
+\r
+                       String sequenceName = scansingle.nextLine().trim();\r
+                       SortedSet<Range> domsR = parseRanges(GlobProtResult.GlobDoms,\r
+                                       scansingle.nextLine());\r
+                       SortedSet<Range> disorderR = parseRanges(GlobProtResult.Disorder,\r
+                                       scansingle.nextLine());\r
+\r
+                       String title = scansingle.nextLine();\r
+                       assert title.startsWith("# RESIDUE      DYDX") : ">Sequence_name must follow column title: # RESIDUE DYDX RAW SMOOTHED!";\r
+\r
+                       while (scansingle.hasNext()) {\r
+                               seqbuffer.append(scansingle.next());\r
+                               dydxScore.add(scansingle.nextFloat());\r
+                               rawScore.add(scansingle.nextFloat());\r
+                               smoothedScore.add(scansingle.nextFloat());\r
+                       }\r
+                       FastaSequence fs = new FastaSequence(sequenceName,\r
+                                       seqbuffer.toString());\r
+                       Set<Score> scores = new HashSet<Score>();\r
+                       scores.add(new Score(GlobProtResult.Disorder, disorderR));\r
+                       scores.add(new Score(GlobProtResult.GlobDoms, domsR));\r
+                       scores.add(new Score(GlobProtResult.Dydx, dydxScore));\r
+                       scores.add(new Score(GlobProtResult.RawScore, rawScore));\r
+                       scores.add(new Score(GlobProtResult.SmoothedScore, smoothedScore));\r
+                       results.put(fs, scores);\r
+\r
+                       scansingle.close();\r
+               }\r
+\r
+               input.close();\r
+               return results;\r
+       }\r
        /**\r
         * Read AACon result with no alignment files. This method leaves incoming\r
         * the InputStream results open!\r
@@ -554,3 +688,20 @@ public final class SequenceUtil {
        }\r
 \r
 }\r
+\r
+enum DisemblResult {\r
+       /** These contains ranges and scores */\r
+       COILS, REM465, HOTLOOPS\r
+}\r
+enum GlobProtResult {\r
+       /** This a range with no scores */\r
+       GlobDoms,\r
+       /** This a range with no scores */\r
+       Disorder,\r
+       /** This a score with no range */\r
+       Dydx,\r
+       /** This a score with no range */\r
+       SmoothedScore,\r
+       /** This a score with no range */\r
+       RawScore\r
+}
\ No newline at end of file

diff --git a/runner/compbio/runner/disorder/GlobPlot.java b/runner/compbio/runner/disorder/GlobPlot.java
new file mode 100644 (file)
index 0000000..6decede
--- /dev/null
+++ b/runner/compbio/runner/disorder/GlobPlot.java
@@ -0,0 +1,145 @@
+/*\r
+ * Copyright (c) 2011 Peter Troshin JAva Bioinformatics Analysis Web Services\r
+ * (JABAWS) @version: 2.0 This library is free software; you can redistribute it\r
+ * and/or modify it under the terms of the Apache License version 2 as published\r
+ * by the Apache Software Foundation This library is distributed in the hope\r
+ * that it will be useful, but WITHOUT ANY WARRANTY; without even the implied\r
+ * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * Apache License for more details. A copy of the license is in\r
+ * apache_license.txt. It is also available here:\r
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt Any republication or\r
+ * derived work distributed in source code form must include this copyright and\r
+ * license notice.\r
+ */\r
+\r
+package compbio.runner.disorder;\r
+\r
+import java.io.File;\r
+import java.io.FileInputStream;\r
+import java.io.FileNotFoundException;\r
+import java.io.IOException;\r
+import java.io.InputStream;\r
+import java.util.Map;\r
+import java.util.Set;\r
+\r
+import org.apache.log4j.Logger;\r
+\r
+import compbio.data.sequence.Score;\r
+import compbio.data.sequence.SequenceUtil;\r
+import compbio.data.sequence.UnknownFileFormatException;\r
+import compbio.engine.client.Executable;\r
+import compbio.engine.client.PipedExecutable;\r
+import compbio.engine.client.SkeletalExecutable;\r
+import compbio.metadata.Limit;\r
+import compbio.metadata.LimitsManager;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.runner.Util;\r
+\r
+/**\r
+ * ./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame\r
+ * \r
+ * FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file'\r
+ * Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file'\r
+ * \r
+ * Hard-coded values are 10 15 74 4 5.\r
+ * \r
+ * Changing these values are not recommended by developers, apart from smoothing\r
+ * window. However, the binary, GlobPlot depends on - Tisean which is not happy\r
+ * with arbitrary changes to these values, so changing them can lead to\r
+ * problems. May be we can offer preset?\r
+ * \r
+ * This is not a standard GlobPlot! The script has been modified!\r
+ * \r
+ */\r
+public class GlobPlot extends SkeletalExecutable<GlobPlot>\r
+               implements\r
+                       PipedExecutable<GlobPlot> {\r
+\r
+       private static Logger log = Logger.getLogger(GlobPlot.class);\r
+\r
+       // Cache for Limits information\r
+       private static LimitsManager<GlobPlot> limits;\r
+\r
+       public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
+\r
+       /* The parameter list there must not contain same values! */\r
+       public GlobPlot() {\r
+               // remove default input to prevent it to appear in the parameters list\r
+               // that could happen if the parameters are set first\r
+               // super.setInput("");\r
+       }\r
+\r
+       @SuppressWarnings("unchecked")\r
+       public Map<String, Set<Score>> getResults(String workDirectory)\r
+                       throws ResultNotAvailableException {\r
+\r
+               InputStream inStream = null;\r
+               Map<String, Set<Score>> results = null;\r
+               // How about getting ranges?\r
+               try {\r
+                       inStream = new FileInputStream(new File(workDirectory, getOutput()));\r
+                       results = SequenceUtil.removeSequences(SequenceUtil\r
+                                       .readDisembl(inStream));\r
+                       inStream.close();\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
+               } catch (UnknownFileFormatException e) {\r
+                       log.error(e.getMessage(), e.getCause());\r
+                       throw new ResultNotAvailableException(e);\r
+               } catch (NullPointerException e) {\r
+                       log.error(e.getMessage(), e.getCause());\r
+                       throw new ResultNotAvailableException(e);\r
+               }\r
+\r
+               return results;\r
+       }\r
+\r
+       @Override\r
+       public GlobPlot setInput(String inFile) {\r
+               super.setInput(inFile);\r
+               cbuilder.setLast(inFile);\r
+               return this;\r
+       }\r
+\r
+       @Override\r
+       public Limit<GlobPlot> getLimit(String presetName) {\r
+               if (limits == null) {\r
+                       limits = getLimits();\r
+               }\r
+\r
+               Limit<GlobPlot> limit = null;\r
+               if (limits != null) {\r
+                       // this returns default limit if preset is undefined!\r
+                       limit = limits.getLimitByName(presetName);\r
+               }\r
+               // If limit is not defined for a particular preset, then return default\r
+               // limit\r
+               if (limit == null) {\r
+                       log.debug("Limit for the preset " + presetName\r
+                                       + " is not found. Using default");\r
+                       limit = limits.getDefaultLimit();\r
+               }\r
+               return limit;\r
+       }\r
+\r
+       @Override\r
+       public LimitsManager<GlobPlot> getLimits() {\r
+               // synchronise on static field\r
+               synchronized (log) {\r
+                       if (limits == null) {\r
+                               limits = Util.getLimits(this.getClass());\r
+                       }\r
+               }\r
+               return limits;\r
+       }\r
+\r
+       @Override\r
+       public Class<? extends Executable<?>> getType() {\r
+               return this.getClass();\r
+       }\r
+\r
+}\r

diff --git a/testsrc/compbio/data/sequence/SequenceUtilTester.java b/testsrc/compbio/data/sequence/SequenceUtilTester.java
index edb57a4..9a8c5a0 100644 (file)
--- a/testsrc/compbio/data/sequence/SequenceUtilTester.java
+++ b/testsrc/compbio/data/sequence/SequenceUtilTester.java
@@ -149,11 +149,11 @@ public class SequenceUtilTester {
        /**\r
         * This test tests the loading of horizontally formatted Jronn output file\r
         * \r
-        * First seq \r
+        * First seq\r
         * \r
-        * M    0.86010 0.88512 0.37094\r
+        * M 0.86010 0.88512 0.37094\r
         * \r
-        * T    0.79983 0.85864 0.44331\r
+        * T 0.79983 0.85864 0.44331\r
         * \r
         */\r
        @SuppressWarnings("unchecked")\r
@@ -163,18 +163,85 @@ public class SequenceUtilTester {
                FileInputStream fio;\r
                try {\r
                        fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
-                                       + "scores.out");\r
+                                       + "disembl.out");\r
                        Map<FastaSequence, Set<Score>> aseqs = SequenceUtil\r
                                        .readDisembl(fio);\r
                        assertNotNull(aseqs);\r
-                       assertEquals(aseqs.size(), 3); \r
+                       assertEquals(aseqs.size(), 3);\r
                        System.out.println(aseqs);\r
-                       for(FastaSequence fs: aseqs.keySet()) {\r
-                               assertTrue(" Foobar_dundeefriends Foobar dundeefriends ".contains(fs.getId()));\r
-                               Set<Score> scores = aseqs.get(fs); \r
-                               assertEquals(scores.size(),3);\r
+                       for (FastaSequence fs : aseqs.keySet()) {\r
+                               assertTrue(" Foobar_dundeefriends Foobar dundeefriends "\r
+                                               .contains(fs.getId()));\r
+                               Set<Score> scores = aseqs.get(fs);\r
+                               assertEquals(scores.size(), 3);\r
                        }\r
-                         fio.close();\r
+                       fio.close();\r
+               } catch (FileNotFoundException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getLocalizedMessage());\r
+               } catch (IOException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getLocalizedMessage());\r
+               } catch (UnknownFileFormatException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getLocalizedMessage());\r
+               }\r
+       }\r
+\r
+       /**\r
+        * This test tests the loading of horizontally formatted Jronn output file\r
+        * \r
+        * First sequence:\r
+        * \r
+        * >Foobar_dundeefriends\r
+        * \r
+        * # GlobDoms 2-358, 373-568\r
+        * \r
+        * # Disorder 1-5, 206-218, 243-250, 288-300, 313-324, 359-372, 475-481\r
+        * \r
+        * # RESIDUE DYDX RAW SMOOTHED\r
+        * \r
+        * M 0.0044 -0.2259 -0.2259\r
+        * \r
+        * T -0.1308 -0.2170 -0.2170\r
+        * \r
+        * ............\r
+        * \r
+        * > Second sequence\r
+        */\r
+       @SuppressWarnings("unchecked")\r
+       @Test\r
+       public void testReadGlobPlotResults() {\r
+\r
+               FileInputStream fio;\r
+               try {\r
+                       fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
+                                       + "globplot.out");\r
+                       Map<FastaSequence, Set<Score>> aseqs = SequenceUtil\r
+                                       .readGlobPlot(fio);\r
+                       assertNotNull(aseqs);\r
+                       assertEquals(aseqs.size(), 3);\r
+\r
+                       FastaSequence fsdf = null;\r
+                       Set<Score> scores = null;\r
+                       for (FastaSequence fs : aseqs.keySet()) {\r
+                               if ("Foobar_dundeefriends".contains(fs.getId())) {\r
+                                       fsdf = fs;\r
+                                       scores = aseqs.get(fs);\r
+                               }\r
+                               assertEquals(scores.size(), 5);\r
+                       }\r
+                       for (Score score : scores) {\r
+                               if (score.getMethod() == GlobProtResult.Disorder) {\r
+                                       assertEquals(score.getRanges().size(), 7);\r
+                                       assertTrue(score.getScores().isEmpty());\r
+                               }\r
+                               if (score.getMethod() == GlobProtResult.Dydx) {\r
+                                       assertFalse(score.getScores().isEmpty());\r
+                                       assertTrue(score.getRanges().isEmpty());\r
+                               }\r
+                       }\r
+                       fio.close();\r
                } catch (FileNotFoundException e) {\r
                        e.printStackTrace();\r
                        fail(e.getLocalizedMessage());\r

diff --git a/testsrc/compbio/runner/disorder/GlobPlotTester.java b/testsrc/compbio/runner/disorder/GlobPlotTester.java
new file mode 100644 (file)
index 0000000..ffafe26
--- /dev/null
+++ b/testsrc/compbio/runner/disorder/GlobPlotTester.java
@@ -0,0 +1,312 @@
+/* Copyright (c) 2009 Peter Troshin\r
+ *  \r
+ *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0     \r
+ * \r
+ *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
+ *  Apache License version 2 as published by the Apache Software Foundation\r
+ * \r
+ *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
+ *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
+ *  License for more details.\r
+ * \r
+ *  A copy of the license is in apache_license.txt. It is also available here:\r
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
+ * \r
+ * Any republication or derived work distributed in source code form\r
+ * must include this copyright and license notice.\r
+ */\r
+\r
+package compbio.runner.disorder;\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
+import java.util.Map;\r
+import java.util.Set;\r
+\r
+import javax.xml.bind.ValidationException;\r
+\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.Score;\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.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.util.SysPrefs;\r
+\r
+public class GlobPlotTester {\r
+\r
+       public static String test_outfile = "TO1381.globprot.out";\r
+\r
+       private GlobPlot globprot;\r
+\r
+       @BeforeMethod(alwaysRun = true)\r
+       void init() {\r
+               globprot = new GlobPlot();\r
+               globprot.setInput(AllTestSuit.test_input).setOutput(test_outfile);\r
+       }\r
+\r
+       @Test(groups = {AllTestSuit.test_group_cluster,\r
+                       AllTestSuit.test_group_runner})\r
+       public void testRunOnCluster() {\r
+               assertFalse(SysPrefs.isWindows,\r
+                               "Cluster execution can only be in unix environment");\r
+               try {\r
+                       ConfiguredExecutable<GlobPlot> confGlobPlot = Configurator\r
+                                       .configureExecutable(globprot,\r
+                                                       Executable.ExecProvider.Cluster);\r
+                       JobRunner runner = JobRunner.getInstance(confGlobPlot);\r
+\r
+                       assertNotNull(runner, "Runner is NULL");\r
+                       runner.executeJob();\r
+                       // assertNotNull("JobId is null", jobId1);\r
+                       JobStatus status = runner.getJobStatus();\r
+                       assertTrue(status == JobStatus.PENDING\r
+                                       || status == JobStatus.RUNNING,\r
+                                       "Status of the process is wrong!");\r
+                       JobInfo info = runner.getJobInfo();\r
+                       assertNotNull(info, "JobInfo is null");\r
+                       StatisticManager sm = new StatisticManager(info);\r
+                       assertNotNull(sm, "Statictic manager is null");\r
+                       try {\r
+\r
+                               String exits = sm.getExitStatus();\r
+                               assertNotNull("Exit status is null", exits);\r
+                               // cut 4 trailing zeros from the number\r
+                               int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)\r
+                                               .intValue();\r
+                               assertEquals(0, exitsInt);\r
+                               System.out.println(sm.getAllStats());\r
+\r
+                       } catch (ParseException e) {\r
+                               e.printStackTrace();\r
+                               fail("Parse Exception: " + e.getMessage());\r
+                       }\r
+                       // assertFalse(runner.cleanup());\r
+                       assertTrue(sm.hasExited());\r
+                       assertFalse(sm.wasAborted());\r
+                       assertFalse(sm.hasDump());\r
+                       assertFalse(sm.hasSignaled());\r
+\r
+               } catch (JobSubmissionException e) {\r
+                       e.printStackTrace();\r
+                       fail("DrmaaException caught:" + e.getMessage());\r
+               } catch (JobExecutionException e) {\r
+                       e.printStackTrace();\r
+                       fail("DrmaaException caught:" + e.getMessage());\r
+               } catch (DrmaaException e) {\r
+                       e.printStackTrace();\r
+                       fail("DrmaaException caught:" + e.getMessage());\r
+               }\r
+       }\r
+\r
+       /**\r
+        * This tests fails from time to time depending on the cluster load or some\r
+        * other factors. Any client code has to adjust for this issue\r
+        */\r
+       @Test(groups = {AllTestSuit.test_group_cluster,\r
+                       AllTestSuit.test_group_runner})\r
+       public void testRunOnClusterAsync() {\r
+               assertFalse(SysPrefs.isWindows,\r
+                               "Cluster execution can only be in unix environment");\r
+               try {\r
+                       ConfiguredExecutable<GlobPlot> confGlobPlot = Configurator\r
+                                       .configureExecutable(globprot,\r
+                                                       Executable.ExecProvider.Cluster);\r
+                       AsyncExecutor aengine = Configurator.getAsyncEngine(confGlobPlot);\r
+                       String jobId = aengine.submitJob(confGlobPlot);\r
+                       assertNotNull(jobId, "Runner is NULL");\r
+                       // let drmaa to start\r
+                       Thread.sleep(500);\r
+                       JobStatus status = aengine.getJobStatus(jobId);\r
+                       while (status != JobStatus.FINISHED) {\r
+                               System.out.println("Job Status: " + status);\r
+                               Thread.sleep(1000);\r
+                               status = aengine.getJobStatus(jobId);\r
+                               ConfiguredExecutable<GlobPlot> result = (ConfiguredExecutable<GlobPlot>) aengine\r
+                                               .getResults(jobId);\r
+                               assertNotNull(result);\r
+                               System.out.println("RES:" + result);\r
+                               // Some times the job could be removed from the cluster\r
+                               // accounting\r
+                               // before it has been reported to finish. Make sure\r
+                               // to stop waiting in such case\r
+                               if (status == JobStatus.UNDEFINED) {\r
+                                       break;\r
+                               }\r
+                       }\r
+               } catch (JobSubmissionException e) {\r
+                       e.printStackTrace();\r
+                       fail("DrmaaException caught:" + e.getMessage());\r
+               } catch (InterruptedException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getMessage());\r
+               } catch (ResultNotAvailableException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getMessage());\r
+               }\r
+       }\r
+\r
+       @Test(groups = {AllTestSuit.test_group_runner})\r
+       public void testRunLocally() {\r
+               try {\r
+                       ConfiguredExecutable<GlobPlot> confGlobPlot = Configurator\r
+                                       .configureExecutable(globprot,\r
+                                                       Executable.ExecProvider.Local);\r
+\r
+                       // For local execution use relative\r
+                       LocalRunner lr = new LocalRunner(confGlobPlot);\r
+                       lr.executeJob();\r
+                       ConfiguredExecutable<?> al1 = lr.waitForResult();\r
+                       assertNotNull(al1.getResults());\r
+                       Map<String, Set<Score>> al2 = confGlobPlot.getResults();\r
+                       assertNotNull(al2);\r
+                       assertEquals(al2.size(), 3);\r
+                       assertEquals(al1.getResults(), al2);\r
+               } catch (JobSubmissionException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getLocalizedMessage());\r
+               } catch (ResultNotAvailableException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getLocalizedMessage());\r
+               } catch (JobExecutionException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getLocalizedMessage());\r
+               }\r
+       }\r
+\r
+       @Test(groups = {AllTestSuit.test_group_runner})\r
+       public void readStatistics() {\r
+               // No execution statistics is available!\r
+       }\r
+\r
+       @Test(groups = {AllTestSuit.test_group_runner})\r
+       public void testPersistance() {\r
+               try {\r
+                       GlobPlot disembl = new GlobPlot();\r
+                       disembl.setError("errrr.txt").setInput(AllTestSuit.test_input)\r
+                                       .setOutput("outtt.txt");\r
+                       assertEquals(disembl.getInput(), AllTestSuit.test_input);\r
+                       assertEquals(disembl.getError(), "errrr.txt");\r
+                       assertEquals(disembl.getOutput(), "outtt.txt");\r
+                       ConfiguredExecutable<GlobPlot> cGlobPlot = Configurator\r
+                                       .configureExecutable(disembl, Executable.ExecProvider.Local);\r
+\r
+                       SyncExecutor sexec = Configurator.getSyncEngine(cGlobPlot);\r
+                       sexec.executeJob();\r
+                       ConfiguredExecutable<?> al = sexec.waitForResult();\r
+                       assertNotNull(al.getResults());\r
+                       // Save run configuration\r
+                       assertTrue(cGlobPlot.saveRunConfiguration());\r
+\r
+                       // See if loaded configuration is the same as saved\r
+                       RunConfiguration loadedRun = RunConfiguration\r
+                                       .load(new FileInputStream(new File(cGlobPlot\r
+                                                       .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
+                       assertEquals(\r
+                                       ((ConfExecutable<GlobPlot>) cGlobPlot)\r
+                                                       .getRunConfiguration(),\r
+                                       loadedRun);\r
+                       // Load run configuration as ConfExecutable\r
+                       ConfiguredExecutable<GlobPlot> resurrectedCGlobPlot = (ConfiguredExecutable<GlobPlot>) cGlobPlot\r
+                                       .loadRunConfiguration(new FileInputStream(new File(\r
+                                                       cGlobPlot.getWorkDirectory(),\r
+                                                       RunConfiguration.rconfigFile)));\r
+                       assertNotNull(resurrectedCGlobPlot);\r
+                       assertEquals(resurrectedCGlobPlot.getExecutable().getInput(),\r
+                                       AllTestSuit.test_input);\r
+                       assertEquals(resurrectedCGlobPlot.getExecutable().getError(),\r
+                                       "errrr.txt");\r
+                       assertEquals(resurrectedCGlobPlot.getExecutable().getOutput(),\r
+                                       "outtt.txt");\r
+                       // See in details whether executables are the same\r
+                       assertEquals(resurrectedCGlobPlot.getExecutable(), disembl);\r
+\r
+                       ConfiguredExecutable<GlobPlot> resGlobPlot = Configurator\r
+                                       .configureExecutable(resurrectedCGlobPlot.getExecutable(),\r
+                                                       Executable.ExecProvider.Local);\r
+\r
+                       sexec = Configurator.getSyncEngine(resGlobPlot,\r
+                                       Executable.ExecProvider.Local);\r
+                       sexec.executeJob();\r
+                       al = sexec.waitForResult();\r
+                       assertNotNull(al);\r
+\r
+               } catch (JobSubmissionException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getMessage());\r
+               } catch (JobExecutionException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getMessage());\r
+               } catch (FileNotFoundException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getMessage());\r
+               } catch (IOException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getMessage());\r
+               } catch (ResultNotAvailableException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getMessage());\r
+               }\r
+       }\r
+\r
+       @Test(groups = {AllTestSuit.test_group_runner})\r
+       public void testConfigurationLoading() {\r
+               try {\r
+                       RunnerConfig<GlobPlot> disemblConfig = ConfExecutable\r
+                                       .getRunnerOptions(GlobPlot.class);\r
+                       assertNotNull(disemblConfig);\r
+                       // There is no disembl parameters\r
+                       assertTrue(disemblConfig.getArguments().size() == 0);\r
+\r
+                       PresetManager<GlobPlot> disemblPresets = ConfExecutable\r
+                                       .getRunnerPresets(GlobPlot.class);\r
+                       assertNull(disemblPresets); // there is no presets\r
+\r
+                       LimitsManager<GlobPlot> disemblLimits = ConfExecutable\r
+                                       .getRunnerLimits(GlobPlot.class);\r
+                       assertNotNull(disemblLimits);\r
+                       assertTrue(disemblLimits.getLimits().size() > 0);\r
+                       disemblLimits.validate(disemblPresets);\r
+\r
+               } catch (FileNotFoundException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getLocalizedMessage());\r
+               } catch (IOException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getLocalizedMessage());\r
+               } catch (ValidationException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getLocalizedMessage());\r
+               }\r
+       }\r
+\r
+}\r

diff --git a/testsrc/testdata/disembl.out b/testsrc/testdata/disembl.out
index 06011cc..cb9301d 100644 (file)
--- a/testsrc/testdata/disembl.out
+++ b/testsrc/testdata/disembl.out
@@ -1,3 +1,7 @@
+> Foobar_dundeefriends
+# COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343, 350-391, 429-485, 497-506, 539-547
+# REM465 355-368
+# HOTLOOPS 
 # RESIDUE COILS REM465 HOTLOOPS
 M      0.86010 0.88512 0.37094
 T      0.79983 0.85864 0.44331
@@ -567,6 +571,10 @@ W  0.36015 0.55044 0.05833
 L      0.47985 0.62475 0.12977
 G      0.69681 0.58187 0.22957
 I      0.79530 0.62112 0.21132
+> Foobar
+# COILS 32-40, 65-73, 85-133, 156-165, 200-256, 263-304, 342-398, 410-419, 452-460
+# REM465 1-11, 268-281
+# HOTLOOPS 100-118
 # RESIDUE COILS REM465 HOTLOOPS
 M      0.79892 0.92921 0.40349
 G      0.74423 0.81900 0.43658
@@ -1049,6 +1057,10 @@ W        0.36015 0.55044 0.05833
 L      0.47985 0.62475 0.12977
 G      0.69681 0.58187 0.22957
 I      0.79530 0.62112 0.21132
+> dundeefriends
+# COILS 33-40, 49-57, 82-90, 99-112, 132-141, 163-192, 215-224, 259-315, 322-363, 401-457, 469-478
+# REM465 327-340
+# HOTLOOPS 162-176
 # RESIDUE COILS REM465 HOTLOOPS
 M      0.86010 0.88512 0.37094
 T      0.79983 0.85864 0.44331

diff --git a/testsrc/testdata/globplot.out b/testsrc/testdata/globplot.out
new file mode 100644 (file)
index 0000000..b64de45
--- /dev/null
+++ b/testsrc/testdata/globplot.out
@@ -0,0 +1,1580 @@
+>Foobar_dundeefriends
+# GlobDoms 2-358, 373-568
+# Disorder 1-5, 206-218, 243-250, 288-300, 313-324, 359-372, 475-481
+# RESIDUE      DYDX    RAW     SMOOTHED
+M      0.0044  -0.2259 -0.2259
+T      -0.1308 -0.2170 -0.2170
+A      0.1138  -0.4786 -0.4786
+D      0.2166  -0.2509 -0.2509
+G      0.2762  0.1823  0.1823
+P      -0.0883 0.7346  0.7346
+R      -0.1023 0.5580  0.5580
+E      -0.1690 0.3533  0.3533
+L      -0.1690 0.0154  0.0154
+L      -0.1690 -0.3225 -0.3225
+Q      -0.1314 -0.5263 -0.5102
+L      -0.1346 -0.7549 -0.8481
+R      -0.1387 -0.9758 -1.0247
+A      -0.1494 -1.2063 -1.2863
+A      -0.1578 -1.4255 -1.5478
+V      -0.1602 -1.6093 -1.9340
+R      -0.1552 -1.7255 -2.1106
+H      -0.1505 -1.8260 -2.1118
+R      -0.1481 -1.9080 -2.2884
+P      -0.1487 -1.9932 -1.7361
+Q      -0.1459 -2.1165 -1.9238
+D      -0.1448 -2.2294 -1.6961
+F      -0.1465 -2.3529 -1.9217
+V      -0.1509 -2.4723 -2.3079
+A      -0.1487 -2.6447 -2.5694
+W      -0.1496 -2.8181 -2.8128
+L      -0.1467 -3.0481 -3.1507
+M      -0.1408 -3.2963 -3.3766
+L      -0.1328 -3.5276 -3.7146
+A      -0.1251 -3.7526 -3.9761
+D      -0.1112 -3.8916 -3.7485
+A      -0.0914 -4.0331 -4.0100
+E      -0.0691 -4.0904 -4.2147
+L      -0.0503 -4.0958 -4.5526
+G      -0.0377 -4.0708 -4.1194
+M      -0.0316 -4.0132 -4.3453
+G      -0.0287 -3.9483 -3.9121
+D      -0.0304 -3.8935 -3.6844
+T      -0.0274 -3.8847 -3.6756
+T      -0.0321 -3.8781 -3.6667
+A      -0.0425 -3.8906 -3.9282
+G      -0.0526 -3.8880 -3.4950
+E      -0.0642 -3.9316 -3.6997
+M      -0.0698 -4.0514 -3.9256
+A      -0.0736 -4.2387 -4.1871
+V      -0.0714 -4.3968 -4.5733
+Q      -0.0648 -4.6000 -4.7610
+R      -0.0553 -4.7368 -4.9376
+G      -0.0456 -4.8141 -4.5043
+L      -0.0400 -4.8435 -4.8423
+A      -0.0362 -4.8415 -5.1038
+L      -0.0366 -4.8415 -5.4418
+H      -0.0336 -4.7825 -5.4430
+P      -0.0253 -4.7554 -4.8907
+G      -0.0207 -4.7156 -4.4574
+H      -0.0230 -4.6639 -4.4586
+P      -0.0313 -4.6408 -3.9063
+E      -0.0438 -4.6396 -4.1110
+A      -0.0569 -4.6841 -4.3726
+V      -0.0648 -4.7102 -4.7587
+A      -0.0777 -4.7733 -5.0203
+R      -0.0945 -4.8800 -5.1969
+L      -0.1142 -5.0570 -5.5348
+G      -0.1358 -5.2672 -5.1016
+R      -0.1503 -5.4680 -5.2782
+V      -0.1591 -5.6478 -5.6643
+R      -0.1675 -5.8306 -5.8409
+W      -0.1690 -5.9581 -6.0843
+T      -0.1725 -6.0822 -6.0754
+Q      -0.1786 -6.2127 -6.2631
+Q      -0.1870 -6.3760 -6.4508
+R      -0.1963 -6.5669 -6.6274
+H      -0.2063 -6.7759 -6.6286
+A      -0.2139 -7.0418 -6.8901
+E      -0.2076 -7.2945 -7.0948
+A      -0.2022 -7.5264 -7.3563
+A      -0.2007 -7.7587 -7.6179
+V      -0.1896 -8.0276 -8.0041
+L      -0.1806 -8.2740 -8.3420
+L      -0.1675 -8.4920 -8.6799
+Q      -0.1460 -8.7199 -8.8676
+Q      -0.1186 -8.9311 -9.0553
+A      -0.0970 -9.0628 -9.3168
+S      -0.0763 -9.1225 -9.1739
+D      -0.0608 -9.1310 -8.9463
+A      -0.0485 -9.1019 -9.2078
+A      -0.0413 -9.0427 -9.4694
+P      -0.0292 -9.0094 -8.9171
+E      -0.0203 -8.9775 -9.1218
+H      -0.0180 -8.9371 -9.1230
+P      -0.0234 -8.9005 -8.5707
+G      -0.0325 -8.8808 -8.1374
+I      -0.0396 -8.9116 -8.5597
+A      -0.0529 -8.9681 -8.8212
+L      -0.0574 -9.0678 -9.1591
+W      -0.0603 -9.1470 -9.4025
+L      -0.0692 -9.2411 -9.7404
+G      -0.0832 -9.3680 -9.3072
+H      -0.0916 -9.4644 -9.3084
+A      -0.1041 -9.5829 -9.5700
+L      -0.1176 -9.7153 -9.9079
+E      -0.1241 -9.8142 -10.1126
+D      -0.1241 -9.8709 -9.8850
+A      -0.1282 -9.9483 -10.1465
+G      -0.1316 -10.0546        -9.7133
+Q      -0.1381 -10.1852        -9.9010
+A      -0.1478 -10.3348        -10.1625
+E      -0.1585 -10.5346        -10.3672
+A      -0.1622 -10.7075        -10.6287
+A      -0.1661 -10.8657        -10.8903
+A      -0.1736 -11.0327        -11.1518
+A      -0.1740 -11.2739        -11.4133
+A      -0.1765 -11.5188        -11.6749
+Y      -0.1748 -11.7334        -11.8824
+T      -0.1657 -11.9933        -11.8735
+R      -0.1500 -12.1756        -12.0501
+A      -0.1386 -12.3069        -12.3116
+H      -0.1266 -12.4283        -12.3128
+Q      -0.1172 -12.5187        -12.5005
+L      -0.1100 -12.5936        -12.8385
+L      -0.1072 -12.6504        -13.1764
+P      -0.1086 -12.6999        -12.6241
+E      -0.1068 -12.7843        -12.8288
+E      -0.1085 -12.8699        -13.0334
+P      -0.1121 -12.9644        -12.4811
+Y      -0.1146 -13.0533        -12.6886
+I      -0.1184 -13.1500        -13.1109
+T      -0.1268 -13.2566        -13.1020
+A      -0.1318 -13.3789        -13.3635
+Q      -0.1328 -13.5388        -13.5512
+L      -0.1387 -13.7143        -13.8891
+L      -0.1487 -13.9215        -14.2271
+N      -0.1515 -14.0861        -13.9972
+W      -0.1578 -14.2523        -14.2406
+R      -0.1600 -14.4605        -14.4172
+R      -0.1559 -14.5985        -14.5937
+R      -0.1545 -14.7201        -14.7703
+L      -0.1524 -14.8781        -15.1083
+C      -0.1495 -15.0103        -15.1234
+D      -0.1483 -15.1427        -14.8958
+W      -0.1504 -15.2619        -15.1392
+R      -0.1551 -15.4013        -15.3158
+A      -0.1635 -15.5628        -15.5773
+L      -0.1678 -15.7048        -15.9152
+D      -0.1757 -15.8518        -15.6876
+V      -0.1843 -16.0133        -16.0738
+L      -0.1926 -16.1954        -16.4117
+S      -0.1926 -16.4320        -16.2688
+A      -0.1980 -16.6718        -16.5304
+Q      -0.1934 -16.9450        -16.7180
+V      -0.1850 -17.1666        -17.1042
+R      -0.1806 -17.3618        -17.2808
+A      -0.1765 -17.5442        -17.5423
+A      -0.1643 -17.7649        -17.8039
+V      -0.1560 -17.9679        -18.1901
+A      -0.1443 -18.1104        -18.4516
+Q      -0.1368 -18.2403        -18.6393
+G      -0.1345 -18.3579        -18.2061
+V      -0.1243 -18.4598        -18.5922
+G      -0.1164 -18.5430        -18.1590
+A      -0.1043 -18.6311        -18.4205
+V      -0.0978 -18.7048        -18.8067
+E      -0.0886 -18.7817        -19.0114
+P      -0.0838 -18.8410        -18.4591
+F      -0.0832 -18.8935        -18.6847
+A      -0.0880 -18.9645        -18.9462
+F      -0.0963 -19.0573        -19.1718
+L      -0.1093 -19.1660        -19.5097
+S      -0.1167 -19.2503        -19.3668
+E      -0.1263 -19.3827        -19.5715
+D      -0.1299 -19.4815        -19.3439
+A      -0.1356 -19.5982        -19.6054
+S      -0.1427 -19.7595        -19.4625
+A      -0.1517 -19.9432        -19.7241
+A      -0.1528 -20.0807        -19.9856
+E      -0.1552 -20.2254        -20.1903
+Q      -0.1603 -20.3794        -20.3780
+L      -0.1698 -20.5376        -20.7159
+A      -0.1828 -20.7297        -20.9774
+C      -0.1927 -20.9215        -20.9926
+A      -0.1986 -21.1583        -21.2541
+R      -0.2017 -21.3621        -21.4307
+T      -0.2054 -21.5805        -21.4218
+R      -0.1946 -21.8196        -21.5984
+A      -0.1872 -22.0304        -21.8600
+Q      -0.1821 -22.2253        -22.0476
+A      -0.1679 -22.4506        -22.3092
+I      -0.1523 -22.6526        -22.7314
+A      -0.1403 -22.8316        -22.9930
+A      -0.1336 -22.9780        -23.2545
+S      -0.1259 -23.0946        -23.1116
+V      -0.1163 -23.2186        -23.4978
+R      -0.1072 -23.3246        -23.6744
+P      -0.0893 -23.4273        -23.1221
+L      -0.0641 -23.5283        -23.4600
+A      -0.0453 -23.5684        -23.7215
+P      -0.0298 -23.5663        -23.1692
+T      -0.0213 -23.5249        -23.1603
+R      -0.0113 -23.5220        -23.3369
+V      -0.0072 -23.5040        -23.7231
+R      -0.0111 -23.4767        -23.8997
+S      -0.0102 -23.4531        -23.7568
+K      -0.0109 -23.4738        -23.8569
+G      -0.0084 -23.5363        -23.4237
+P      -0.0016 -23.5309        -22.8714
+L      0.0063  -23.5629        -23.2093
+R      0.0063  -23.5848        -23.3859
+V      0.0136  -23.5575        -23.7721
+G      0.0282  -23.5419        -23.3388
+F      0.0398  -23.5068        -23.5644
+V      0.0505  -23.5029        -23.9506
+S      0.0523  -23.4715        -23.8077
+N      0.0501  -23.4058        -23.5778
+G      0.0454  -23.3568        -23.1446
+F      0.0406  -23.2606        -23.3702
+G      0.0400  -23.1123        -22.9369
+A      0.0311  -22.9758        -23.1985
+H      0.0176  -22.8641        -23.1997
+P      -0.0032 -22.8087        -22.6474
+T      -0.0205 -22.7510        -22.6385
+G      -0.0439 -22.7364        -22.2053
+L      -0.0735 -22.8028        -22.5432
+L      -0.1019 -22.9191        -22.8812
+T      -0.1274 -23.0739        -22.8723
+V      -0.1467 -23.2403        -23.2584
+A      -0.1590 -23.5027        -23.5200
+L      -0.1598 -23.7667        -23.8579
+F      -0.1663 -24.0344        -24.0835
+E      -0.1727 -24.3050        -24.2882
+A      -0.1714 -24.5257        -24.5497
+L      -0.1661 -24.7373        -24.8876
+Q      -0.1552 -24.8728        -25.0753
+R      -0.1472 -24.9927        -25.2519
+R      -0.1427 -25.1024        -25.4285
+Q      -0.1335 -25.1947        -25.6162
+P      -0.1233 -25.3008        -25.0639
+D      -0.1072 -25.4241        -24.8362
+L      -0.0901 -25.5466        -25.1742
+Q      -0.0710 -25.6561        -25.3619
+M      -0.0475 -25.7581        -25.5878
+H      -0.0250 -25.8314        -25.5890
+L      -0.0069 -25.8787        -25.9269
+F      0.0040  -25.8787        -26.1525
+A      0.0101  -25.8574        -26.4140
+T      0.0139  -25.8368        -26.4051
+S      0.0125  -25.8141        -26.2623
+G      0.0145  -25.7262        -25.8290
+D      0.0173  -25.5971        -25.6014
+D      0.0144  -25.4789        -25.3738
+G      0.0068  -25.3685        -24.9405
+S      -0.0006 -25.3037        -24.7977
+T      -0.0069 -25.2567        -24.7888
+L      -0.0214 -25.2360        -25.1267
+R      -0.0381 -25.2708        -25.3033
+T      -0.0549 -25.3831        -25.2944
+R      -0.0765 -25.5151        -25.4710
+L      -0.0953 -25.6884        -25.8090
+A      -0.1106 -25.8544        -26.0705
+Q      -0.1253 -26.0173        -26.2582
+A      -0.1288 -26.2179        -26.5197
+S      -0.1239 -26.3853        -26.3768
+T      -0.1187 -26.5054        -26.3679
+L      -0.1134 -26.5926        -26.7059
+H      -0.1091 -26.6929        -26.7071
+D      -0.1076 -26.7797        -26.4795
+V      -0.1038 -26.8519        -26.8656
+T      -0.0991 -26.9263        -26.8568
+A      -0.1015 -26.9916        -27.1183
+L      -0.1065 -27.0724        -27.4562
+G      -0.1110 -27.1786        -27.0230
+H      -0.1162 -27.3159        -27.0242
+L      -0.1111 -27.4743        -27.3622
+A      -0.1091 -27.5925        -27.6237
+T      -0.1060 -27.7451        -27.6148
+A      -0.1053 -27.8685        -27.8764
+K      -0.1031 -27.9475        -27.9765
+H      -0.1060 -28.0390        -27.9777
+I      -0.1028 -28.1459        -28.3999
+R      -0.1049 -28.2461        -28.5765
+H      -0.1113 -28.3685        -28.5777
+H      -0.1031 -28.4886        -28.5789
+G      -0.0954 -28.5713        -28.1457
+I      -0.0839 -28.6855        -28.5679
+D      -0.0686 -28.8162        -28.3403
+L      -0.0463 -28.9301        -28.6782
+L      -0.0217 -29.0352        -29.0162
+F      -0.0011 -29.0778        -29.2418
+D      0.0265  -29.0999        -29.0141
+L      0.0443  -29.0805        -29.3521
+R      0.0533  -29.0122        -29.5287
+G      0.0585  -28.9098        -29.0954
+W      0.0595  -28.7809        -29.3388
+G      0.0620  -28.5919        -28.9056
+G      0.0568  -28.4241        -28.4723
+G      0.0623  -28.2793        -28.0391
+G      0.0595  -28.1365        -27.6059
+R      0.0589  -28.0622        -27.7825
+P      0.0487  -27.9900        -27.2302
+E      0.0382  -27.9138        -27.4349
+V      0.0173  -27.8738        -27.8210
+F      -0.0038 -27.9160        -28.0466
+A      -0.0228 -27.9597        -28.3081
+L      -0.0499 -28.0548        -28.6461
+R      -0.0743 -28.1644        -28.8227
+P      -0.0944 -28.2838        -28.2704
+A      -0.0994 -28.4432        -28.5319
+P      -0.0911 -28.5985        -27.9796
+V      -0.0837 -28.7475        -28.3658
+Q      -0.0652 -28.8342        -28.5534
+V      -0.0423 -28.9150        -28.9396
+N      -0.0272 -28.9569        -28.7097
+W      -0.0074 -29.0112        -28.9531
+L      0.0053  -29.0259        -29.2910
+A      0.0100  -29.0268        -29.5526
+Y      0.0148  -29.0449        -29.7601
+P      0.0239  -28.9906        -29.2078
+G      0.0244  -28.9152        -28.7745
+T      0.0286  -28.7696        -28.7657
+S      0.0343  -28.6707        -28.6228
+G      0.0407  -28.5865        -28.1895
+A      0.0380  -28.5067        -28.4511
+P      0.0353  -28.4008        -27.8988
+W      0.0260  -28.3088        -28.1421
+M      0.0077  -28.2515        -28.3680
+D      -0.0069 -28.2944        -28.1404
+Y      -0.0181 -28.4246        -28.3479
+V      -0.0265 -28.5206        -28.7341
+L      -0.0339 -28.5809        -29.0720
+G      -0.0435 -28.6470        -28.6388
+D      -0.0433 -28.7546        -28.4112
+A      -0.0399 -28.8101        -28.6727
+F      -0.0419 -28.8677        -28.8983
+A      -0.0335 -28.8878        -29.1598
+L      -0.0298 -28.8953        -29.4978
+P      -0.0281 -28.9123        -28.9454
+P      -0.0271 -28.8815        -28.3931
+A      -0.0317 -28.8459        -28.6547
+L      -0.0421 -28.8442        -28.9926
+E      -0.0600 -28.8783        -29.1973
+P      -0.0725 -28.9058        -28.6450
+F      -0.0736 -28.9652        -28.8705
+Y      -0.0796 -29.0336        -29.0780
+S      -0.0895 -29.1221        -28.9352
+E      -0.1034 -29.2457        -29.1398
+H      -0.1127 -29.4629        -29.1411
+V      -0.1114 -29.6606        -29.5272
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+
+
+>Foobar
+# GlobDoms 5-271, 286-481
+# Disorder 1-6, 119-131, 156-163, 201-213, 226-237, 272-285, 388-394
+# RESIDUE      DYDX    RAW     SMOOTHED
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+I      -0.2111 -34.5400        -34.5400
+
+
+>dundeefriends
+# GlobDoms 2-330, 345-513
+# Disorder 1-5, 178-190, 215-222, 260-272, 285-296, 331-344, 447-453
+# RESIDUE      DYDX    RAW     SMOOTHED
+M      0.0044  -0.2259 -0.2259
+T      -0.1308 -0.2170 -0.2170
+A      0.1138  -0.4786 -0.4786
+D      0.2166  -0.2509 -0.2509
+G      0.2762  0.1823  0.1823
+P      -0.0883 0.7346  0.7346
+R      -0.1023 0.5580  0.5580
+E      -0.1690 0.3533  0.3533
+L      -0.1690 0.0154  0.0154
+L      -0.1690 -0.3225 -0.3225
+Q      -0.1314 -0.5263 -0.5102
+L      -0.1346 -0.7549 -0.8481
+R      -0.1408 -0.9669 -1.0247
+A      -0.1517 -1.2003 -1.2863
+A      -0.1601 -1.4240 -1.5478
+V      -0.1637 -1.6071 -1.9340
+R      -0.1582 -1.7315 -2.1106
+H      -0.1547 -1.8330 -2.1118
+R      -0.1522 -1.9226 -2.2884
+P      -0.1462 -2.0425 -1.7361
+Q      -0.1439 -2.1574 -1.9238
+D      -0.1424 -2.2663 -1.6961
+V      -0.1456 -2.3773 -2.0823
+A      -0.1411 -2.5309 -2.3438
+W      -0.1397 -2.6796 -2.5872
+L      -0.1326 -2.8678 -2.9251
+M      -0.1254 -3.0823 -3.1511
+L      -0.1185 -3.2925 -3.4890
+A      -0.1099 -3.4840 -3.7505
+D      -0.1054 -3.6527 -3.5229
+A      -0.0856 -3.7822 -3.7844
+E      -0.0691 -3.8648 -3.9891
+L      -0.0503 -3.8702 -4.3270
+G      -0.0377 -3.8452 -3.8938
+M      -0.0316 -3.7876 -4.1197
+G      -0.0287 -3.7227 -3.6865
+D      -0.0304 -3.6679 -3.4589
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+M      -0.0698 -3.8258 -3.7000
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+R      -0.1503 -5.2424 -5.0526
+V      -0.1591 -5.4223 -5.4388
+R      -0.1675 -5.6050 -5.6154
+W      -0.1690 -5.7325 -5.8587
+T      -0.1725 -5.8566 -5.8499
+Q      -0.1786 -5.9872 -6.0375
+Q      -0.1870 -6.1504 -6.2252
+R      -0.1963 -6.3413 -6.4018
+H      -0.2063 -6.5504 -6.4030
+A      -0.2139 -6.8162 -6.6646
+E      -0.2076 -7.0689 -6.8692
+A      -0.2022 -7.3008 -7.1308
+A      -0.2007 -7.5331 -7.3923
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+H      -0.0408 -33.2442        -33.1220
+L      -0.0332 -33.2631        -33.4599
+G      -0.0313 -33.2700        -33.0267
+L      -0.0341 -33.2719        -33.3647
+D      -0.0438 -33.3012        -33.1370
+E      -0.0611 -33.3554        -33.3417
+M      -0.0742 -33.3977        -33.5676
+N      -0.0842 -33.4514        -33.3377
+V      -0.0998 -33.5430        -33.7239
+A      -0.1147 -33.6285        -33.9854
+D      -0.1296 -33.7326        -33.7578
+D      -0.1453 -33.8509        -33.5302
+A      -0.1652 -34.0195        -33.7917
+A      -0.1729 -34.2019        -34.0533
+F      -0.1782 -34.4416        -34.2788
+V      -0.1695 -34.7003        -34.6650
+A      -0.1638 -34.9368        -34.9265
+K      -0.1615 -35.1606        -35.0266
+A      -0.1569 -35.3347        -35.2882
+V      -0.1537 -35.5276        -35.6744
+A      -0.1540 -35.7168        -35.9359
+L      -0.1519 -35.8629        -36.2738
+A      -0.1423 -35.9778        -36.5354
+S      -0.1352 -36.0717        -36.3925
+D      -0.1296 -36.1558        -36.1648
+P      -0.1277 -36.2188        -35.6125
+A      -0.1237 -36.3187        -35.8741
+A      -0.1246 -36.4057        -36.1356
+L      -0.1272 -36.4798        -36.4735
+T      -0.1315 -36.5688        -36.4647
+A      -0.1393 -36.6882        -36.7262
+L      -0.1496 -36.8344        -37.0641
+H      -0.1589 -37.0401        -37.0654
+A      -0.1742 -37.2651        -37.3269
+R      -0.1931 -37.5035        -37.5035
+V      0.1138  -37.8897        -37.8897
+D      -0.1931 -37.6620        -37.6620
+V      -0.1690 -38.0482        -38.0482
+L      -0.0883 -38.3861        -38.3861
+R      -0.0883 -38.5627        -38.5627
+R      -0.1023 -38.7393        -38.7393
+E      0.0714  -38.9440        -38.9440
+S      -0.2111 -38.8011        -38.8011
+I      -0.2111 -39.2234        -39.2234
+
+

diff --git a/webservices/compbio/ws/server/GlobPlotWS.java b/webservices/compbio/ws/server/GlobPlotWS.java
new file mode 100644 (file)
index 0000000..df402fa
--- /dev/null
+++ b/webservices/compbio/ws/server/GlobPlotWS.java
@@ -0,0 +1,157 @@
+package compbio.ws.server;\r
+\r
+import java.util.HashMap;\r
+import java.util.HashSet;\r
+import java.util.List;\r
+\r
+import javax.annotation.Resource;\r
+import javax.jws.WebService;\r
+import javax.xml.ws.WebServiceContext;\r
+\r
+import org.apache.log4j.Logger;\r
+\r
+import compbio.data.msa.SequenceAnnotation;\r
+import compbio.data.sequence.FastaSequence;\r
+import compbio.data.sequence.Score;\r
+import compbio.engine.AsyncExecutor;\r
+import compbio.engine.Configurator;\r
+import compbio.engine.client.ConfiguredExecutable;\r
+import compbio.metadata.ChunkHolder;\r
+import compbio.metadata.JobStatus;\r
+import compbio.metadata.JobSubmissionException;\r
+import compbio.metadata.Limit;\r
+import compbio.metadata.LimitExceededException;\r
+import compbio.metadata.LimitsManager;\r
+import compbio.metadata.Option;\r
+import compbio.metadata.Preset;\r
+import compbio.metadata.PresetManager;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.metadata.RunnerConfig;\r
+import compbio.metadata.UnsupportedRuntimeException;\r
+import compbio.metadata.WrongParameterException;\r
+import compbio.runner.Util;\r
+import compbio.runner.disorder.GlobPlot;\r
+\r
+@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "GlobPlotWS")\r
+public class GlobPlotWS implements SequenceAnnotation<GlobPlot> {\r
+\r
+       // Ask for resource injection\r
+       @Resource\r
+       WebServiceContext wsContext;\r
+\r
+       private static Logger statLog = Logger.getLogger("GlobPlotWS-stats");\r
+\r
+       private static Logger log = Logger.getLogger(GlobPlotWS.class);\r
+\r
+       private static final RunnerConfig<GlobPlot> globPlotOptions = Util\r
+                       .getSupportedOptions(GlobPlot.class);\r
+\r
+       private static final PresetManager<GlobPlot> globPlotPresets = Util\r
+                       .getPresets(GlobPlot.class);\r
+\r
+       ConfiguredExecutable<GlobPlot> init(List<FastaSequence> sequences)\r
+                       throws JobSubmissionException {\r
+               GlobPlot globPlot = new GlobPlot();\r
+               globPlot.setInput("fasta.in").setOutput("globPlot.out");\r
+               return Configurator.configureExecutable(globPlot, sequences);\r
+       }\r
+\r
+       @Override\r
+       public HashMap<String, HashSet<Score>> getAnnotation(String jobId)\r
+                       throws ResultNotAvailableException {\r
+               WSUtil.validateJobId(jobId);\r
+               AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
+               ConfiguredExecutable<GlobPlot> globPlot = (ConfiguredExecutable<GlobPlot>) asyncEngine\r
+                               .getResults(jobId);\r
+               HashMap<String, HashSet<Score>> mas = globPlot.getResults();\r
+               log.trace(jobId + " getConservation : " + mas);\r
+               return mas;\r
+       }\r
+\r
+       @Override\r
+       public Limit<GlobPlot> getLimit(String presetName) {\r
+               return new GlobPlot().getLimit(presetName);\r
+       }\r
+\r
+       @Override\r
+       public LimitsManager<GlobPlot> getLimits() {\r
+               return new GlobPlot().getLimits();\r
+       }\r
+\r
+       @Override\r
+       public ChunkHolder pullExecStatistics(String jobId, long position) {\r
+               // Execution stat is not supported\r
+               return new ChunkHolder("", -1);\r
+       }\r
+\r
+       @Override\r
+       public boolean cancelJob(String jobId) {\r
+               WSUtil.validateJobId(jobId);\r
+               return WSUtil.cancelJob(jobId);\r
+       }\r
+\r
+       @Override\r
+       public JobStatus getJobStatus(String jobId) {\r
+               WSUtil.validateJobId(jobId);\r
+               return WSUtil.getJobStatus(jobId);\r
+       }\r
+\r
+       @Override\r
+       public PresetManager<GlobPlot> getPresets() {\r
+               return globPlotPresets;\r
+       }\r
+\r
+       @Override\r
+       public RunnerConfig<GlobPlot> getRunnerOptions() {\r
+               return globPlotOptions;\r
+       }\r
+\r
+       String analize(List<FastaSequence> sequences,\r
+                       ConfiguredExecutable<GlobPlot> confExec, Logger log, String method,\r
+                       Limit<GlobPlot> limit) throws JobSubmissionException {\r
+               if (limit != null && limit.isExceeded(sequences)) {\r
+                       throw LimitExceededException.newLimitExceeded(limit, sequences);\r
+               }\r
+\r
+               compbio.runner.Util.writeInput(sequences, confExec);\r
+               AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
+               String jobId = engine.submitJob(confExec);\r
+               return jobId;\r
+       }\r
+\r
+       @Override\r
+       public String analize(List<FastaSequence> sequences)\r
+                       throws UnsupportedRuntimeException, LimitExceededException,\r
+                       JobSubmissionException {\r
+               WSUtil.validateFastaInput(sequences);\r
+               ConfiguredExecutable<GlobPlot> confGlobPlot = init(sequences);\r
+\r
+               return analize(sequences, confGlobPlot, null, "analize", getLimit(""));\r
+       }\r
+\r
+       /*\r
+        * No options are supported, thus the result of this call will be as simple\r
+        * call to analize without parameters\r
+        */\r
+       @Override\r
+       public String customAnalize(List<FastaSequence> sequences,\r
+                       List<Option<GlobPlot>> options) throws UnsupportedRuntimeException,\r
+                       LimitExceededException, JobSubmissionException,\r
+                       WrongParameterException {\r
+               return analize(sequences);\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<GlobPlot> preset) throws UnsupportedRuntimeException,\r
+                       LimitExceededException, JobSubmissionException,\r
+                       WrongParameterException {\r
+\r
+               return analize(sequences);\r
+       }\r
+\r
+}\r