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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
test
/
Test.java
diff --git
a/forester/java/src/org/forester/test/Test.java
b/forester/java/src/org/forester/test/Test.java
index
1a8a216
..
9cda7b7
100644
(file)
--- a/
forester/java/src/org/forester/test/Test.java
+++ b/
forester/java/src/org/forester/test/Test.java
@@
-5627,13
+5627,13
@@
public final class Test {
private static boolean testGeneralMsaParser() {
try {
final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
private static boolean testGeneralMsaParser() {
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 Msa msa_0 = GeneralMsaParser.parseMsa( new ByteArrayInputStream( msa_str_0.getBytes() ) );
final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 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 Msa msa_1 = GeneralMsaParser.parseMsa( new ByteArrayInputStream( msa_str_1.getBytes() ) );
final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
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 Msa msa_2 = GeneralMsaParser.parseMsa( new ByteArrayInputStream( msa_str_2.getBytes() ) );
final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
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() ) );
+ final Msa msa_3 = GeneralMsaParser.parseMsa( new ByteArrayInputStream( msa_str_3.getBytes() ) );
if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
return false;
}
if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
return false;
}
@@
-5670,7
+5670,7
@@
public final class Test {
if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
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" ) );
+ final Msa msa_4 = GeneralMsaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
return false;
}
if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
return false;
}
@@
-5680,7
+5680,7
@@
public final class Test {
if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
return false;
}
if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
return false;
}
- final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
+ final Msa msa_5 = GeneralMsaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
return false;
}
if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
return false;
}
@@
-5690,7
+5690,7
@@
public final class Test {
if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
return false;
}
if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
return false;
}
- final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
+ final Msa msa_6 = GeneralMsaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
return false;
}
if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
return false;
}