removed unneeded import

[jalview.git] / forester / java / src / org / forester / util / ForesterUtil.java

diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java
index dc89976..f144a81 100644 (file)
--- a/forester/java/src/org/forester/util/ForesterUtil.java
+++ b/forester/java/src/org/forester/util/ForesterUtil.java
@@ -542,15 +542,16 @@ public final class ForesterUtil {
     }
 
     final public static MolecularSequence.TYPE guessMolecularSequenceType( final String mol_seq ) {
-        if ( mol_seq.contains( "L" ) || mol_seq.contains( "I" ) || mol_seq.contains( "E" ) || mol_seq.contains( "H" )
-                || mol_seq.contains( "D" ) || mol_seq.contains( "Q" ) ) {
+        final String s = mol_seq.toUpperCase();
+        if ( s.contains( "L" ) || s.contains( "I" ) || s.contains( "E" ) || s.contains( "H" ) || s.contains( "D" )
+                || s.contains( "Q" ) ) {
             return TYPE.AA;
         }
         else {
-            if ( mol_seq.contains( "T" ) ) {
+            if ( s.contains( "T" ) ) {
                 return TYPE.DNA;
             }
-            else if ( mol_seq.contains( "U" ) ) {
+            else if ( s.contains( "U" ) ) {
                 return TYPE.RNA;
             }
         }
@@ -722,7 +723,7 @@ public final class ForesterUtil {
         }
         return null;
     }
-    
+
     final public static String isWritableFile( final String s ) {
         return isWritableFile( new File( s ) );
     }
@@ -1517,7 +1518,7 @@ public final class ForesterUtil {
             is.close();
         }
         catch ( final Exception e ) {
-            // ignore  
+            // ignore
         }
         return trees;
     }
@@ -1549,7 +1550,7 @@ public final class ForesterUtil {
         File the_one = null;
         do {
             int matches = 0;
-            for( File file : files ) {
+            for( final File file : files ) {
                 if ( file.getName().startsWith( my_prefix ) ) {
                     matches++;
                     if ( matches > 1 ) {
@@ -1597,6 +1598,24 @@ public final class ForesterUtil {
         return a.substring( 0, min_length );
     }
 
+    public final static boolean isContainsPrefix( final String word, final String prefix, final String separator ) {
+        if ( ForesterUtil.isEmpty( separator ) ) {
+            throw new IllegalArgumentException( "separator must not be null or empty" );
+        }
+        final String[] word_ary = word.split( Pattern.quote( separator ) );
+        final String[] prefix_ary = prefix.split( Pattern.quote( separator ) );
+        if ( word_ary.length < prefix_ary.length ) {
+            return false;
+        }
+        final int prefix_ary_length = prefix_ary.length;
+        for( int i = 0; i < prefix_ary_length; ++i ) {
+            if ( !( word_ary[ i ].equals( prefix_ary[ i ] ) ) ) {
+                return false;
+            }
+        }
+        return true;
+    }
+
     public final static String greatestCommonPrefix( final String a, final String b, final String separator ) {
         if ( ForesterUtil.isEmpty( separator ) ) {
             throw new IllegalArgumentException( "separator must not be null or empty" );
@@ -1606,7 +1625,7 @@ public final class ForesterUtil {
         final int min_length = Math.min( as.length, bs.length );
         for( int i = 0; i < min_length; ++i ) {
             if ( !( as[ i ].equals( bs[ i ] ) ) ) {
-                StringBuilder sb = new StringBuilder();
+                final StringBuilder sb = new StringBuilder();
                 boolean first = true;
                 for( int j = 0; j < i; ++j ) {
                     if ( first ) {
@@ -1620,7 +1639,7 @@ public final class ForesterUtil {
                 return sb.toString();
             }
         }
-        StringBuilder sb = new StringBuilder();
+        final StringBuilder sb = new StringBuilder();
         boolean first = true;
         for( int j = 0; j < min_length; ++j ) {
             if ( first ) {
@@ -1665,9 +1684,6 @@ public final class ForesterUtil {
         return common;
     }
 
-    private ForesterUtil() {
-    }
-
     public static List<String> spliIntoPrefixes( final String prefix, final String separator ) {
         final String[] a = prefix.split( Pattern.quote( separator ) );
         final List<String> l = new ArrayList<String>();
@@ -1679,15 +1695,16 @@ public final class ForesterUtil {
                     sb.append( separator );
                 }
             }
-            //  System.out.println( sb.toString() );
             l.add( sb.toString() );
         }
         return l;
     }
 
-    //
     public static boolean isLooksLikeFasta( final File file ) throws IOException {
         final String first_line = ForesterUtil.getFirstLine( file ).trim().toLowerCase();
         return ( ( !isEmptyTrimmed( first_line ) && first_line.trim().startsWith( ">" ) ) );
     }
+
+    private ForesterUtil() {
+    }
 }