in progress

[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 5864f61..22253df 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -6376,13 +6376,15 @@ public final class Test {
             final Writer w = new StringWriter();
             dmsa2.write( w, MSA_FORMAT.PHYLIP );
             final String phylip = w.toString();
-            if ( !phylip.equals( "new_c x" + ForesterUtil.LINE_SEPARATOR ) ) {
+            if ( !phylip.equals( "1 1" + ForesterUtil.LINE_SEPARATOR + "new_c x" + ForesterUtil.LINE_SEPARATOR ) ) {
+                System.out.println( phylip );
                 return false;
             }
             final Writer w2 = new StringWriter();
             dmsa2.write( w2, MSA_FORMAT.FASTA );
             final String fasta = w2.toString();
             if ( !fasta.equals( ">new_c" + ForesterUtil.LINE_SEPARATOR + "x" + ForesterUtil.LINE_SEPARATOR ) ) {
+                System.out.println( fasta );
                 return false;
             }
         }
@@ -11322,7 +11324,6 @@ public final class Test {
                 }
                 return false;
             }
-            //
             id = SequenceAccessionTools.parseAccessorFromString( "segmented worms|gb_ADF31344" );
             if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
                     || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
@@ -11332,7 +11333,6 @@ public final class Test {
                 }
                 return false;
             }
-            //
             id = SequenceAccessionTools.parseAccessorFromString( "segmented worms gb_ADF31344 and more" );
             if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
                     || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
@@ -11342,7 +11342,6 @@ public final class Test {
                 }
                 return false;
             }
-            // 
             id = SequenceAccessionTools.parseAccessorFromString( "gb_AAA96518_1" );
             if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
                     || !id.getValue().equals( "AAA96518" ) || !id.getSource().equals( "ncbi" ) ) {
@@ -11352,7 +11351,6 @@ public final class Test {
                 }
                 return false;
             }
-            // 
             id = SequenceAccessionTools.parseAccessorFromString( "gb_EHB07727_1_rodents_" );
             if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
                     || !id.getValue().equals( "EHB07727" ) || !id.getSource().equals( "ncbi" ) ) {
@@ -11362,7 +11360,6 @@ public final class Test {
                 }
                 return false;
             }
-            // 
             id = SequenceAccessionTools.parseAccessorFromString( "dbj_BAF37827_1_turtles_" );
             if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
                     || !id.getValue().equals( "BAF37827" ) || !id.getSource().equals( "ncbi" ) ) {
@@ -11372,7 +11369,6 @@ public final class Test {
                 }
                 return false;
             }
-            // 
             id = SequenceAccessionTools.parseAccessorFromString( "emb_CAA73223_1_primates_" );
             if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
                     || !id.getValue().equals( "CAA73223" ) || !id.getSource().equals( "ncbi" ) ) {
@@ -11382,7 +11378,6 @@ public final class Test {
                 }
                 return false;
             }
-            // 
             id = SequenceAccessionTools.parseAccessorFromString( "mites|ref_XP_002434188_1" );
             if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
                     || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
@@ -11392,7 +11387,6 @@ public final class Test {
                 }
                 return false;
             }
-            // 
             id = SequenceAccessionTools.parseAccessorFromString( "mites_ref_XP_002434188_1_bla_XP_12345" );
             if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
                     || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
@@ -11402,7 +11396,6 @@ public final class Test {
                 }
                 return false;
             }
-            // 
             id = SequenceAccessionTools.parseAccessorFromString( "P4A123" );
             if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
                     || !id.getValue().equals( "P4A123" ) || !id.getSource().equals( "uniprot" ) ) {
@@ -11418,6 +11411,40 @@ public final class Test {
                 System.out.println( "provider=" + id.getSource() );
                 return false;
             }
+            //
+            id = SequenceAccessionTools.parseAccessorFromString( "N3B004Z009" );
+            if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
+                    || !id.getValue().equals( "N3B004Z009" ) || !id.getSource().equals( "uniprot" ) ) {
+                if ( id != null ) {
+                    System.out.println( "value   =" + id.getValue() );
+                    System.out.println( "provider=" + id.getSource() );
+                }
+                return false;
+            }
+            id = SequenceAccessionTools.parseAccessorFromString( "A4CAA4ZBB9" );
+            if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
+                    || !id.getValue().equals( "A4CAA4ZBB9" ) || !id.getSource().equals( "uniprot" ) ) {
+                if ( id != null ) {
+                    System.out.println( "value   =" + id.getValue() );
+                    System.out.println( "provider=" + id.getSource() );
+                }
+                return false;
+            }
+            id = SequenceAccessionTools.parseAccessorFromString( "ecoli_A4CAA4ZBB9_rt" );
+            if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
+                    || !id.getValue().equals( "A4CAA4ZBB9" ) || !id.getSource().equals( "uniprot" ) ) {
+                if ( id != null ) {
+                    System.out.println( "value   =" + id.getValue() );
+                    System.out.println( "provider=" + id.getSource() );
+                }
+                return false;
+            }
+            id = SequenceAccessionTools.parseAccessorFromString( "Q4CAA4ZBB9" );
+            if ( id != null ) {
+                System.out.println( "value   =" + id.getValue() );
+                System.out.println( "provider=" + id.getSource() );
+                return false;
+            }
         }
         catch ( final Exception e ) {
             e.printStackTrace( System.out );