in progress

diff --git a/forester/java/src/org/forester/msa/Mafft.java b/forester/java/src/org/forester/msa/Mafft.java
index 0cdaac2..b56ca1e 100644 (file)
--- a/forester/java/src/org/forester/msa/Mafft.java
+++ b/forester/java/src/org/forester/msa/Mafft.java
@@ -50,7 +50,7 @@ public final class Mafft implements MsaInferrer {
     }
 
     private static String getPathToCmd() {
-        //TODO this needs to come from env variable, etc.
+        //TODO this needs to come from config file!!
         //FIXME ..
         //should not be in this class!
         String path = "";
@@ -62,7 +62,7 @@ public final class Mafft implements MsaInferrer {
             path = "C:\\Program Files\\mafft-win\\mafft.bat";
         }
         else {
-            path = "/home/czmasek/SOFTWARE/MSA/MAFFT/mafft-6.864-without-extensions/scripts/mafft";
+            path = "/home/czmasek/bin/mafft";
         }
         return path;
     }
@@ -109,15 +109,17 @@ public final class Mafft implements MsaInferrer {
         my_opts.add( path_to_input_seqs.getAbsolutePath() );
         final SystemCommandExecutor command_executor = new SystemCommandExecutor( my_opts );
         final int _exit_code = command_executor.executeCommand();
+        final StringBuilder stderr = command_executor.getStandardErrorFromCommand();
+        _error = stderr.toString();
         if ( _exit_code != 0 ) {
-            throw new IOException( "MAFFT program failed, exit code: " + _exit_code + ", command: " + my_opts );
+            throw new IOException( "MAFFT program failed, exit code: " + _exit_code + "\nCommand:\n" + my_opts
+                    + "\nError:\n" + stderr );
         }
         final StringBuilder stdout = command_executor.getStandardOutputFromCommand();
-        final StringBuilder stderr = command_executor.getStandardErrorFromCommand();
         if ( ( stdout == null ) || ( stdout.length() < 2 ) ) {
-            throw new IOException( "MAFFT program did not produce any output, command: " + my_opts );
+            throw new IOException( "MAFFT program did not produce any output\nCommand:\n" + my_opts + "\nError:\n"
+                    + stderr );
         }
-        _error = stderr.toString();
         final Msa msa = FastaParser.parseMsa( stdout.toString() );
         return msa;
     }

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index fae52db..adcbac9 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -8211,12 +8211,48 @@ public final class Test {
         try {
             final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
             final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
-            final String msa_str_1 = "seq_1 abc\nseq2 ghi\nseq_1 def\nseq2 jkm\n";
+            final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
             final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
             final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
             final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
             final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
             final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
+            if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
+                return false;
+            }
+            if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
+                return false;
+            }
+            if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
+                return false;
+            }
+            if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
+                return false;
+            }
+            if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
+                return false;
+            }
+            if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
+                return false;
+            }
+            if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
+                return false;
+            }
+            if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
+                return false;
+            }
+            if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
+                return false;
+            }
+            if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
+                return false;
+            }
+            if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
+                return false;
+            }
+            if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
+                return false;
+            }
             final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
             if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
                 return false;
@@ -8265,7 +8301,10 @@ public final class Test {
             Msa msa = null;
             final MsaInferrer mafft = Mafft.createInstance();
             msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
-            if ( ( msa == null ) || ( msa.getLength() < 10 ) || ( msa.getNumberOfSequences() != 19 ) ) {
+            if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
+                return false;
+            }
+            if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
                 return false;
             }
         }

diff --git a/forester/java/src/org/forester/util/SystemCommandExecutor.java b/forester/java/src/org/forester/util/SystemCommandExecutor.java
index bb87989..6160382 100644 (file)
--- a/forester/java/src/org/forester/util/SystemCommandExecutor.java
+++ b/forester/java/src/org/forester/util/SystemCommandExecutor.java
@@ -38,7 +38,6 @@ import java.util.List;
 public class SystemCommandExecutor {
 
     private final List<String>    _command_information;
-    private final String          _admin_password;
     private ThreadedStreamHandler _input_stream_handler;
     private ThreadedStreamHandler _error_stream_handler;
     private final static boolean  DEBUG = false;
@@ -63,11 +62,10 @@ public class SystemCommandExecutor {
      */
     public SystemCommandExecutor( final List<String> command_information ) {
         if ( ( command_information == null ) || command_information.isEmpty() ) {
-            throw new IllegalArgumentException( "The commandInformation is required." );
+            throw new IllegalArgumentException( "command information is required" );
         }
         checkCmdFile( new File( command_information.get( 0 ) ) );
         _command_information = command_information;
-        _admin_password = null;
     }
 
     public static boolean isExecuteableFile( final File path_to_cmd_f ) {
@@ -114,9 +112,8 @@ public class SystemCommandExecutor {
             // these need to run as java threads to get the standard output and error from the command.
             // the inputstream handler gets a reference to our stdOutput in case we need to write
             // something to it, such as with the sudo command
-            _input_stream_handler = new ThreadedStreamHandler( inputStream, stdOutput, _admin_password );
+            _input_stream_handler = new ThreadedStreamHandler( inputStream, stdOutput );
             _error_stream_handler = new ThreadedStreamHandler( errorStream );
-            // TODO the inputStreamHandler has a nasty side-effect of hanging if the given password is wrong; fix it
             _input_stream_handler.start();
             _error_stream_handler.start();
             // TODO a better way to do this?
@@ -134,9 +131,9 @@ public class SystemCommandExecutor {
             // generated by process.waitFor() call
             throw e;
         }
-        //  finally {
+        // finally {
         return exit_value;
-        //  }
+        // }
     }
 
     /**

diff --git a/forester/java/src/org/forester/util/ThreadedStreamHandler.java b/forester/java/src/org/forester/util/ThreadedStreamHandler.java
index ed70e75..a8a91e8 100644 (file)
--- a/forester/java/src/org/forester/util/ThreadedStreamHandler.java
+++ b/forester/java/src/org/forester/util/ThreadedStreamHandler.java
@@ -81,6 +81,13 @@ class ThreadedStreamHandler extends Thread {
         sudoIsRequested = true;
     }
 
+    ThreadedStreamHandler( final InputStream inputStream, final OutputStream outputStream ) {
+        this.inputStream = inputStream;
+        this.outputStream = outputStream;
+        printWriter = new PrintWriter( outputStream );
+        sudoIsRequested = false;
+    }
+
     private void doSleep( final long millis ) {
         try {
             Thread.sleep( millis );