JAL-3067 Initial preparation.

diff --git a/.classpath b/.classpath
index 5cb0080..8ca06f2 100644 (file)
--- a/.classpath
+++ b/.classpath
@@ -16,26 +16,9 @@
        <classpathentry kind="lib" path="lib/castor-1.1-cycle-xml.jar" sourcepath="C:/Documents and Settings/JimP/workspace-3.3/castor/src/main/java"/>
        <classpathentry kind="lib" path="lib/JGoogleAnalytics_0.3.jar" sourcepath="/JGoogleAnalytics/src/main/java"/>
        <classpathentry kind="lib" path="lib/vamsas-client.jar"/>
-       <classpathentry kind="lib" path="lib/commons-logging-1.1.1.jar"/>
        <classpathentry kind="lib" path="lib/apache-mime4j-0.6.jar" sourcepath="G:/InstallsDir/Sources for Development/apache-mime4j-0.6-src.zip"/>
-       <classpathentry kind="lib" path="lib/httpclient-4.0.3.jar">
-               <attributes>
-                       <attribute name="javadoc_location" value="file:/D:/InstallsDir/Sources for Development/httpconnect/httpcomponents-client-4.0.3/javadoc/"/>
-               </attributes>
-       </classpathentry>
-       <classpathentry kind="lib" path="lib/httpcore-4.0.1.jar">
-               <attributes>
-                       <attribute name="javadoc_location" value="file:/D:/InstallsDir/Sources for Development/httpconnect/httpcomponents-client-4.0.3/javadoc/"/>
-               </attributes>
-       </classpathentry>
-       <classpathentry kind="lib" path="lib/httpmime-4.0.3.jar">
-               <attributes>
-                       <attribute name="javadoc_location" value="file:/D:/InstallsDir/Sources for Development/httpconnect/httpcomponents-client-4.0.3/javadoc/"/>
-               </attributes>
-       </classpathentry>
        <classpathentry kind="lib" path="lib/miglayout-4.0-swing.jar"/>
        <classpathentry kind="lib" path="lib/jswingreader-0.3.jar" sourcepath="/jswingreader"/>
-       <classpathentry kind="lib" path="lib/commons-codec-1.3.jar"/>
        <classpathentry kind="lib" path="lib/spring-core-3.0.5.RELEASE.jar"/>
        <classpathentry kind="lib" path="lib/spring-web-3.0.5.RELEASE.jar"/>
        <classpathentry kind="lib" path="lib/jabaws-min-client-2.2.0.jar" sourcepath="/clustengine"/>
@@ -61,7 +44,6 @@
        <classpathentry kind="lib" path="lib/jetty-util-9.2.10.v20150310.jar"/>
        <classpathentry kind="lib" path="lib/jetty-http-9.2.10.v20150310.jar"/>
        <classpathentry kind="lib" path="lib/jetty-io-9.2.10.v20150310.jar"/>
-       <classpathentry kind="lib" path="lib/java-json.jar"/>
        <classpathentry kind="lib" path="lib/Jmol-14.6.4_2016.10.26.jar"/>
        <classpathentry kind="con" path="org.testng.TESTNG_CONTAINER"/>
        <classpathentry kind="lib" path="lib/biojava-core-4.1.0.jar"/>
@@ -69,5 +51,13 @@
        <classpathentry kind="lib" path="lib/htsjdk-2.12.0.jar"/>
        <classpathentry kind="lib" path="lib/groovy-all-2.4.12-indy.jar"/>
        <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
+       <classpathentry kind="lib" path="lib/commons-codec-1.10.jar"/>
+       <classpathentry kind="lib" path="lib/commons-logging-1.2.jar"/>
+       <classpathentry kind="lib" path="lib/httpclient-4.5.6.jar"/>
+       <classpathentry kind="lib" path="lib/httpcore-4.4.10.jar"/>
+       <classpathentry kind="lib" path="lib/httpmime-4.5.6.jar"/>
+       <classpathentry kind="lib" path="lib/json-20180130.jar"/>
+       <classpathentry kind="lib" path="D:/mmwarowny/eclipse_ws/slivka-java-client/target/slivkaclient-0.0.1-SNAPSHOT.jar"/>
+       <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
        <classpathentry kind="output" path="classes"/>
 </classpath>

diff --git a/.project b/.project
index 60d0c20..d0dfc7e 100644 (file)
--- a/.project
+++ b/.project
@@ -6,7 +6,7 @@
        </projects>
        <buildSpec>
                <buildCommand>
-                       <name>net.sf.j2s.core.java2scriptbuilder</name>
+                       <name>org.eclipse.jdt.core.javabuilder</name>
                        <arguments>
                        </arguments>
                </buildCommand>

diff --git a/examples/estrogenReceptorProtein.fa b/examples/estrogenReceptorProtein.fa
index 0541d39..8d7f928 100644 (file)
--- a/examples/estrogenReceptorProtein.fa
+++ b/examples/estrogenReceptorProtein.fa
@@ -1,4 +1,4 @@
->UNIPROT|Q7LCB3/1-530 estrogen nuclear receptor beta variant a
+>UNIPROT|Q7LCB3/1-530 estrogen receptor 2 isoform A
 MDIKNSPSSLNSPSSYNCSQSILPLEHGSIYIPSSYVDSHHEYPAMTFYSPAVMNYSIPSNVTNLEGGPGRQ
 TTSPNVLWPTPGHLSPLVVHRQLSHLYAEPQKSPWCEARSLEHTLPVNRETLKRKVSGNRCASPVTGPGSKR
 DAHFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMVK
@@ -7,14 +7,29 @@ FTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDL
 VLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNA
 VTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNAHVLRGCK
 SSITGSECSPAEDSKSKEGSQNPQSQ
->UNIPROT|Q9VSE9/1-484 GH28308p
-MSDGVSILHIKQEVDTPSASCFSPSSKSTATQSGTNGLKSSPSVSPERQLCSSTTSLSCDLHNVSLSNDGDS
-LKGSGTSGGNGGGGGGGTSGGNATNASAGAGSGSVRDELRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ
-GNIEYTCPANNECEINKRRRKACQACRFQKCLLMGMLKEGVRLDRVRGGRQKYRRNPVSNSYQTMQLLYQSN
-TTSLCDVKILEVLNSYEPDALSVQTPPPQVHTTSITNDEASSSSGSIKLESSVVTPNGTCIFQNNNNNDPNE
-ILSVLSDIYDKELVSVIGWAKQIPGFIDLPLNDQMKLLQVSWAEILTLQLTFRSLPFNGKLCFATDVWMDEH
-LAKECGYTEFYYHCVQIAQRMERISPRREEYYLLKALLLANCDILLDDQSSLRAFRDTILNSLNDVVYLLRH
-SSAVSHQQQLLLLLPSLRQADDILRRFWRGIARDEVITMKKLFLEMLEPLAR
+>UNIPROT|Q90ZM7/1-438 corticoid receptor
+GVEFQLPYSASATSFRPSVATSSASGISNFSNGNNFGFLSPNGVQQDGFPYPGFTSPAQSSVPPQKACLICS
+DEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCIQAGMTLGARKLKKQG
+RVKGENQRSPASSTATTSSATPQPSSNSTAVTTFSPPPTGEPIFSPTLIAILQAIEPEVVMSGYDNTRSQTT
+AYMLSSLNRLCDKQLVSIVKWAKSLPGFRNLHIDDQMVLIQYSWMGLMSFAMSWRSFQHTNSKLLYFAPDLV
+FDETRMQQSAMYQLCVEMRQVSEDFMKLQVTSEEFLCMKAILLLSTVPQEGLKSQGCFEEMRISYIRELNRT
+IARTEKNAVQCWQRFYQLTKLLXCMQDLVSKLLEFCFATFTQTQVWSVEFPDMMAEIISAQLASHHGREARA
+LHFHKK
+>UNIPROT|Q90ZM8/1-554 estrogen receptor
+ARGFSEAHGYEYSGASLYQPLPPSCTEFSIGAHQQQQHQHQHHQHQHQQHHHQQQQQQPQPQQNGVLGEGQS
+SHLSYLPPSTELPQYVPSSPSAPYSMELGAGRPHGYDPGPQSLYRGGVESSAPPYSEQQQVVGGGGAMSAMG
+LTEPRHVSSGSLPSSTRPERSTQFCAVCSDYASGYHYGVWSCEGCKAFFKRSTQGHNDYMCPATNQCTIDRN
+RRKSCQACRLRKCYEVGMVKGVRKDRKGFRGVKHKRKRPIPQKNGGEGGAGGGQDVSETRPQGERPSGPRDR
+ESAVSSLEADQVISALLEAEPPTVLSSYDPDKPVTEASLMAALTSLADRELVHMITWAKKIPGFTAIGLSDQ
+VQLLECCWLEILIVGLIWRSIDRPGQLHFAPNLILGREDARNVEGMLDMFDMLLVTVSRFRELHLRREEYVC
+LKAMILLNSGVFFCLSNSAGEQTNVQLIQQILEKVMDALGSTIGHIEASPPQHSRRLSQLLLLLSQIRHISN
+KGIEHLNSMKRKNVIPLYDLLLELLDAHSLQNTGLRTSPPPQDFRATLVP
+>UNIPROT|Q91445/1-344 androgen receptor
+EASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGARKLKKLGN
+LKAQDDIEGASSSSPTEEQAPKLVMTRIDGYECQPIFLNVLEAIEPGVVCAGHDNSQPDSFSNLLTSLNELG
+ERQLVYVVKWAKALPGFRNLHVDDQMSIIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHKSRM
+YSQCIRMRHLSQEFGWLQITPQGFLCMKALLFFSIIPVDGLKNQKLFDELRMNYIKELDRIIACKRKNPTSC
+SRRFYQLTKVLDSVTPIAKDLHQFTFDLLIKAHMVSVDYPEMMAEIISVQVPKILS
 >UNIPROT|Q9IBD5/1-710 progesterone receptor
 MDNNHQDKMESLYTPARASPTPDAESIKRARNLIKTYSESFGSYVEEIVRDDSNNIQSLSSVPLLMRNFGNM
 DTLTCAPGSGSDSEIWKDFVVPGNSVVSKDTCGHVEISTKAENLSWAAAPLSREETLAKGTVTVPATVPKES
@@ -26,15 +41,14 @@ SLTPRRLSGDSQALMPLGCLPGVRELHLSPQIISVLESIEPEVVYSGYDNSQPDMPNMLLNSLNRLCERQLL
 RIVKWSKSLPGFRSLHINDQMALIQYSWMSLMVFSLGWRSFQNVTSDYLYFAPDLILNEEYMRRSPIFDLCM
 AMQFIPQEFANLQVTKEEFLCMKVLLLLNTVPLEGLKSQPQFDEMRQNYIHELTKAIHLRENGVVACSQRFY
 HLTKLMDHMHDIVKKLHLYCLSTFIQADAMRVEFPEMMSEVIASQLPRVLAGMVKPLLFHTK
->UNIPROT|Q7LCB3/1-530 estrogen receptor 2 isoform A
-MDIKNSPSSLNSPSSYNCSQSILPLEHGSIYIPSSYVDSHHEYPAMTFYSPAVMNYSIPSNVTNLEGGPGRQ
-TTSPNVLWPTPGHLSPLVVHRQLSHLYAEPQKSPWCEARSLEHTLPVNRETLKRKVSGNRCASPVTGPGSKR
-DAHFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMVK
-CGSRRERCGYRLVRRQRSADEQLHCAGKAKRSGGHAPRVRELLLDALSPEQLVLTLLEAEPPHVLISRPSAP
-FTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDL
-VLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNA
-VTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNAHVLRGCK
-SSITGSECSPAEDSKSKEGSQNPQSQ
+>UNIPROT|Q9VSE9/1-484 estrogen-related receptor
+MSDGVSILHIKQEVDTPSASCFSPSSKSTATQSGTNGLKSSPSVSPERQLCSSTTSLSCDLHNVSLSNDGDS
+LKGSGTSGGNGGGGGGGTSGGNATNASAGAGSGSVRDELRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ
+GNIEYTCPANNECEINKRRRKACQACRFQKCLLMGMLKEGVRLDRVRGGRQKYRRNPVSNSYQTMQLLYQSN
+TTSLCDVKILEVLNSYEPDALSVQTPPPQVHTTSITNDEASSSSGSIKLESSVVTPNGTCIFQNNNNNDPNE
+ILSVLSDIYDKELVSVIGWAKQIPGFIDLPLNDQMKLLQVSWAEILTLQLTFRSLPFNGKLCFATDVWMDEH
+LAKECGYTEFYYHCVQIAQRMERISPRREEYYLLKALLLANCDILLDDQSSLRAFRDTILNSLNDVVYLLRH
+SSAVSHQQQLLLLLPSLRQADDILRRFWRGIARDEVITMKKLFLEMLEPLAR
 >UNIPROT|Q9YGV9/1-848 androgen receptor alpha
 MEIPVGLGGVSDATNAVFRGPYQNVFHSLQVAFQSHGAVSRSLDFPNTKYGFLQNRHFCEMRQENKQPPCKG
 LGLFYGNHRNSDTGTNEDDIACFSRQSDAEARPGIFSESSLDTGDEITCKLQSDNQGVRASGPLLPGSSGCN
@@ -48,34 +62,3 @@ GQGQGPAEAELSVSPKYDLGFHTQSMFLNILEAIEPEVVNAGHDYGQPDSAASLLTSLNELGERQLVKVVKW
 AKGMPGFRSLYVDDQMTVIQHSWMAVMVFALGWRSFKNVKSRMLYFAPDLVFNEHRMQVSTMYEHCIRMKNF
 SQEFAMLQVSQEEFLCMKALLLFSTIPVEGLKGQNFFDELRRSYINELDRLVSFRSKSSCSERFQQLTRLLD
 SLQPVLKKLHQFTFDLFVQSQNLSNQVCFPEMISEIISVHVPKILAGTVKPILFHK
->UNIPROT|Q90ZM7/1-438 corticoid receptor
-GVEFQLPYSASATSFRPSVATSSASGISNFSNGNNFGFLSPNGVQQDGFPYPGFTSPAQSSVPPQKACLICS
-DEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCIQAGMTLGARKLKKQG
-RVKGENQRSPASSTATTSSATPQPSSNSTAVTTFSPPPTGEPIFSPTLIAILQAIEPEVVMSGYDNTRSQTT
-AYMLSSLNRLCDKQLVSIVKWAKSLPGFRNLHIDDQMVLIQYSWMGLMSFAMSWRSFQHTNSKLLYFAPDLV
-FDETRMQQSAMYQLCVEMRQVSEDFMKLQVTSEEFLCMKAILLLSTVPQEGLKSQGCFEEMRISYIRELNRT
-IARTEKNAVQCWQRFYQLTKLLXCMQDLVSKLLEFCFATFTQTQVWSVEFPDMMAEIISAQLASHHGREARA
-LHFHKK
->UNIPROT|Q91445/1-344 androgen receptor
-EASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGARKLKKLGN
-LKAQDDIEGASSSSPTEEQAPKLVMTRIDGYECQPIFLNVLEAIEPGVVCAGHDNSQPDSFSNLLTSLNELG
-ERQLVYVVKWAKALPGFRNLHVDDQMSIIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHKSRM
-YSQCIRMRHLSQEFGWLQITPQGFLCMKALLFFSIIPVDGLKNQKLFDELRMNYIKELDRIIACKRKNPTSC
-SRRFYQLTKVLDSVTPIAKDLHQFTFDLLIKAHMVSVDYPEMMAEIISVQVPKILS
->UNIPROT|Q9VSE9/1-484 estrogen-related receptor
-MSDGVSILHIKQEVDTPSASCFSPSSKSTATQSGTNGLKSSPSVSPERQLCSSTTSLSCDLHNVSLSNDGDS
-LKGSGTSGGNGGGGGGGTSGGNATNASAGAGSGSVRDELRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ
-GNIEYTCPANNECEINKRRRKACQACRFQKCLLMGMLKEGVRLDRVRGGRQKYRRNPVSNSYQTMQLLYQSN
-TTSLCDVKILEVLNSYEPDALSVQTPPPQVHTTSITNDEASSSSGSIKLESSVVTPNGTCIFQNNNNNDPNE
-ILSVLSDIYDKELVSVIGWAKQIPGFIDLPLNDQMKLLQVSWAEILTLQLTFRSLPFNGKLCFATDVWMDEH
-LAKECGYTEFYYHCVQIAQRMERISPRREEYYLLKALLLANCDILLDDQSSLRAFRDTILNSLNDVVYLLRH
-SSAVSHQQQLLLLLPSLRQADDILRRFWRGIARDEVITMKKLFLEMLEPLAR
->UNIPROT|Q90ZM8/1-554 estrogen receptor
-ARGFSEAHGYEYSGASLYQPLPPSCTEFSIGAHQQQQHQHQHHQHQHQQHHHQQQQQQPQPQQNGVLGEGQS
-SHLSYLPPSTELPQYVPSSPSAPYSMELGAGRPHGYDPGPQSLYRGGVESSAPPYSEQQQVVGGGGAMSAMG
-LTEPRHVSSGSLPSSTRPERSTQFCAVCSDYASGYHYGVWSCEGCKAFFKRSTQGHNDYMCPATNQCTIDRN
-RRKSCQACRLRKCYEVGMVKGVRKDRKGFRGVKHKRKRPIPQKNGGEGGAGGGQDVSETRPQGERPSGPRDR
-ESAVSSLEADQVISALLEAEPPTVLSSYDPDKPVTEASLMAALTSLADRELVHMITWAKKIPGFTAIGLSDQ
-VQLLECCWLEILIVGLIWRSIDRPGQLHFAPNLILGREDARNVEGMLDMFDMLLVTVSRFRELHLRREEYVC
-LKAMILLNSGVFFCLSNSAGEQTNVQLIQQILEKVMDALGSTIGHIEASPPQHSRRLSQLLLLLSQIRHISN
-KGIEHLNSMKRKNVIPLYDLLLELLDAHSLQNTGLRTSPPPQDFRATLVP

diff --git a/lib/commons-codec-1.10.jar b/lib/commons-codec-1.10.jar
new file mode 100644 (file)
index 0000000..1d7417c
Binary files /dev/null and b/lib/commons-codec-1.10.jar differ

diff --git a/lib/commons-codec-1.3.jar b/lib/commons-codec-1.3.jar
deleted file mode 100644 (file)
index 957b675..0000000
Binary files a/lib/commons-codec-1.3.jar and /dev/null differ

diff --git a/lib/commons-logging-1.1.1.jar b/lib/commons-logging-1.1.1.jar
deleted file mode 100644 (file)
index 1deef14..0000000
Binary files a/lib/commons-logging-1.1.1.jar and /dev/null differ

diff --git a/lib/commons-logging-1.2.jar b/lib/commons-logging-1.2.jar
new file mode 100644 (file)
index 0000000..93a3b9f
Binary files /dev/null and b/lib/commons-logging-1.2.jar differ

diff --git a/lib/httpclient-4.0.3.jar b/lib/httpclient-4.0.3.jar
deleted file mode 100644 (file)
index fd0d377..0000000
Binary files a/lib/httpclient-4.0.3.jar and /dev/null differ

diff --git a/lib/httpclient-4.5.6.jar b/lib/httpclient-4.5.6.jar
new file mode 100644 (file)
index 0000000..56231de
Binary files /dev/null and b/lib/httpclient-4.5.6.jar differ

diff --git a/lib/httpcore-4.0.1.jar b/lib/httpcore-4.0.1.jar
deleted file mode 100644 (file)
index 4aef35e..0000000
Binary files a/lib/httpcore-4.0.1.jar and /dev/null differ

diff --git a/lib/httpcore-4.4.10.jar b/lib/httpcore-4.4.10.jar
new file mode 100644 (file)
index 0000000..dc510f8
Binary files /dev/null and b/lib/httpcore-4.4.10.jar differ

diff --git a/lib/httpmime-4.0.3.jar b/lib/httpmime-4.0.3.jar
deleted file mode 100644 (file)
index 0dfd331..0000000
Binary files a/lib/httpmime-4.0.3.jar and /dev/null differ

diff --git a/lib/httpmime-4.5.6.jar b/lib/httpmime-4.5.6.jar
new file mode 100644 (file)
index 0000000..df5a7d1
Binary files /dev/null and b/lib/httpmime-4.5.6.jar differ

diff --git a/lib/java-json.jar b/lib/java-json.jar
deleted file mode 100755 (executable)
index 2f211e3..0000000
Binary files a/lib/java-json.jar and /dev/null differ

diff --git a/lib/json-20180130.jar b/lib/json-20180130.jar
new file mode 100644 (file)
index 0000000..bc2cd41
Binary files /dev/null and b/lib/json-20180130.jar differ

diff --git a/src/Main.java b/src/Main.java
new file mode 100644 (file)
index 0000000..2723feb
--- /dev/null
+++ b/src/Main.java
@@ -0,0 +1,95 @@
+import java.io.File;
+import java.io.IOException;
+import java.net.URISyntaxException;
+
+import uk.ac.dundee.compbio.slivkaclient.FileHandler;
+import uk.ac.dundee.compbio.slivkaclient.HttpException;
+import uk.ac.dundee.compbio.slivkaclient.ServerError;
+import uk.ac.dundee.compbio.slivkaclient.Service;
+import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
+import uk.ac.dundee.compbio.slivkaclient.TaskHandler;
+import uk.ac.dundee.compbio.slivkaclient.form.Form;
+import uk.ac.dundee.compbio.slivkaclient.form.FormField;
+import uk.ac.dundee.compbio.slivkaclient.form.FormValidationException;
+import uk.ac.dundee.compbio.slivkaclient.form.ValidationException;
+
+public class Main
+{
+  public static void main(String[] args)
+  {
+    SlivkaClient cli;
+    try
+    {
+      cli = new SlivkaClient("localhost", 8000);
+    } catch (URISyntaxException e)
+    {
+      throw new Error(e);
+    }
+
+    Service service = null;
+    Form form;
+    try
+    {
+      for (Service s : cli.getServices())
+      {
+        if (s.getName().equals("Clustalw"))
+        {
+          service = s;
+        }
+      }
+      form = service.getForm();
+    } catch (IOException | ServerError | HttpException e)
+    {
+      throw new Error(e);
+    }
+
+    File input = new File("examples/estrogenReceptorProtein.fa");
+    if (!input.exists())
+    {
+      throw new Error("no file");
+    }
+
+    TaskHandler th;
+    try
+    {
+      FileHandler fh = cli.uploadFile(input, "text/plain", "input.txt");
+      th = form.create()
+              .insert("input", fh)
+              .insert("matrix", "blosum")
+              .insert("outorder", "aligned")
+              .submit();
+    } catch (IOException | HttpException | ServerError e)
+    {
+      throw new Error(e);
+    } catch (FormValidationException e)
+    {
+      for (ValidationException e1 : e.getErrors())
+      {
+        System.err.println(e1);
+      }
+      throw new Error(e);
+    }
+
+    try
+    {
+      while (!th.getStatus().isReady())
+      {
+        Thread.sleep(1000);
+      }
+    } catch (IOException | HttpException | Error | InterruptedException e)
+    {
+      throw new Error(e);
+    }
+    try
+    {
+      for (FileHandler fh : th.getResult())
+      {
+        System.out.println(fh.getTitle());
+        fh.writeTo(System.out);
+      }
+    } catch (IOException | HttpException | ServerError e)
+    {
+      throw new Error(e);
+    }
+  }
+}