testsrc/compbio/ws/client/AAConWSClientExample.java

   1 package compbio.ws.client;\r
   2 \r
   3 import java.io.ByteArrayInputStream;\r
   4 import java.io.FileNotFoundException;\r
   5 import java.io.IOException;\r
   6 import java.util.List;\r
   7 \r
   8 import compbio.data.msa.SequenceAnnotation;\r
   9 import compbio.data.sequence.FastaSequence;\r
  10 import compbio.data.sequence.ScoreManager;\r
  11 import compbio.data.sequence.SequenceUtil;\r
  12 import compbio.metadata.JobSubmissionException;\r
  13 import compbio.metadata.Preset;\r
  14 import compbio.metadata.PresetManager;\r
  15 import compbio.metadata.ResultNotAvailableException;\r
  16 import compbio.metadata.UnsupportedRuntimeException;\r
  17 import compbio.metadata.WrongParameterException;\r
  18 import compbio.runner.conservation.AACon;\r
  19 \r
  20 /**\r
  21  * AAConWS client example\r
  22  */\r
  23 public class AAConWSClientExample {\r
  24 \r
  25         /*\r
  26          * Input sequences. For the simplicity keep them in the class\r
  27          */\r
  28         static final String input = ">Foo      \r\n"\r
  29                         + "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\r\n"\r
  30                         + "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL\r\n"\r
  31                         + "LPEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVAQGVGAVEPFAFLSEDASAAEQLAC\r\n"\r
  32                         + "ARTRAQAIAASVRPLAPTRVRSKGPLRVGFVSNGFGAHPTGLLTVALFEALQRRQPDLQM\r\n"\r
  33                         + "HLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHGIDLLFDLRGWGGGGRPEV\r\n"\r
  34                         + "FALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVLRLQGAFQPSDTSR\r\n"\r
  35                         + "VVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLLSGPGEADA\r\n"\r
  36                         + "RLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVL\r\n"\r
  37                         + "TTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRES\r\n"\r
  38                         + "GVFEMDGFADDFGALLQALARRHGWLGI\r\n"\r
  39                         + "\r\n"\r
  40                         + ">Bar                    \r\n"\r
  41                         + "-----------------------------------MGDTTAGEMAVQRGLALH-------\r\n"\r
  42                         + "---------QQRHAEAAVLLQQASDAAPEHPGIALWL-HALEDAGQAEAAAA-YTRAHQL\r\n"\r
  43                         + "LPEEPYITAQLLN--------------------AVAQGVGAVEPFAFLSEDASAAE----\r\n"\r
  44                         + "----------SVRPLAPTRVRSKGPLRVGFVSNGFGAHPTGLLTVALFEALQRRQPDLQM\r\n"\r
  45                         + "HLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHGIDLLFDLRGWGGGGRPEV\r\n"\r
  46                         + "FALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVLRLQGAFQPSDTSR\r\n"\r
  47                         + "VVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLLSGPGEADA\r\n"\r
  48                         + "RLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVL\r\n"\r
  49                         + "TTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRES\r\n"\r
  50                         + "GVFEMDGFADDFGALLQALARRHGWLGI\r\n"\r
  51                         + "\r\n"\r
  52                         + ">Noname             \r\n"\r
  53                         + "-MTADGPRELLQLRAAVRHRPQDVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\r\n"\r
  54                         + "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALED--------------HQL\r\n"\r
  55                         + "LPEEPYITAQLDVLSAQVR-------------AAVAQGVGAVEPFAFLSEDASAAEQLAC\r\n"\r
  56                         + "ARTRAQAIAASVRPLAPTRVRSKGPLRVGFVSNGFGAHPTGLLTVALFEALQRRQPDLQM\r\n"\r
  57                         + "HLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHGIDLLFDLRGWGGGGRPEV\r\n"\r
  58                         + "FALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVLRLQGAFQPSDTSR\r\n"\r
  59                         + "VVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLLSGPGEADA\r\n"\r
  60                         + "RLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVL\r\n"\r
  61                         + "TTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRES\r\n"\r
  62                         + "I---------------------------";\r
  63 \r
  64         public static void main(String[] args) throws UnsupportedRuntimeException,\r
  65                         JobSubmissionException, WrongParameterException,\r
  66                         FileNotFoundException, IOException, ResultNotAvailableException,\r
  67                         InterruptedException {\r
  68 \r
  69                 /*\r
  70                  * Annotation interface for AAConWS web service instance\r
  71                  */\r
  72                 SequenceAnnotation<AACon> client = (SequenceAnnotation<AACon>) Jws2Client\r
  73                                 .connect("http://www.compbio.dundee.ac.uk/aacon",\r
  74                                                 Services.AAConWS);\r
  75 \r
  76                 /* Get the list of available presets */\r
  77                 PresetManager presetman = client.getPresets();\r
  78 \r
  79                 /* Get the Preset object by preset name */\r
  80                 Preset preset = presetman.getPresetByName("Complete conservation");\r
  81 \r
  82                 /*\r
  83                  * Load sequences in FASTA format from the file You can use something\r
  84                  * like new FileInputStream() to load sequence from the file\r
  85                  */\r
  86                 List<FastaSequence> fastalist = SequenceUtil\r
  87                                 .readFasta(new ByteArrayInputStream(input.getBytes()));\r
  88 \r
  89                 /*\r
  90                  * Submit loaded sequences for an alignment using preset. The job\r
  91                  * identifier is returned by this method, you can retrieve the results\r
  92                  * with it sometime later.\r
  93                  */\r
  94                 String jobId = client.presetAnalize(fastalist, preset);\r
  95 \r
  96                 /* This method will block for the duration of the calculation */\r
  97                 ScoreManager result = client.getAnnotation(jobId);\r
  98 \r
  99                 /*\r
 100                  * This is a better way of obtaining results, it does not involve\r
 101                  * holding the connection open for the duration of the calculation,\r
 102                  * Besides, as the University of Dundee public server will reset the\r
 103                  * connection after 10 minutes of idling, this is the only way to obtain\r
 104                  * the results of long running task from our public server.\r
 105                  */\r
 106                 // while (client.getJobStatus(jobId) != JobStatus.FINISHED) {\r
 107                 // Thread.sleep(1000); // wait a second, then recheck the status\r
 108                 // }\r
 109 \r
 110                 /* Output the alignment to standard out */\r
 111                 IOHelper.writeOut(System.out, result);\r
 112                 // Score.write(result, System.out);\r
 113 \r
 114                 /* Alternatively, you can record retrieved alignment into the file */\r
 115                 // FileOutputStream out = new FileOutputStream("result.txt");\r
 116                 // Score.write(result, out);\r
 117                 // out.close();\r
 118         }\r
 119 }\r