X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Futil%2FForesterUtil.java;h=f144a81684894675f7a3442a03586b1560e9b619;hb=5642da5f473ab9ae57fee86c0cb3b33525a2e916;hp=2374654d19297adb20161d476cc769c5c4dcb966;hpb=3929e5396afcdc3c79e7e4421c9fd444bb2e7a1b;p=jalview.git diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java index 2374654..f144a81 100644 --- a/forester/java/src/org/forester/util/ForesterUtil.java +++ b/forester/java/src/org/forester/util/ForesterUtil.java @@ -99,7 +99,7 @@ public final class ForesterUtil { public final static String OS_VERSION = System.getProperty( "os.version" ); public static final String PDB = "http://www.pdb.org/pdb/explore/explore.do?pdbId="; public final static String UNIPROT_KB = "http://www.uniprot.org/uniprot/"; - public final static double ZERO_DIFF = 1.0E-9; + public final static double ZERO_DIFF = 1.0E-12; private static final Pattern PARANTHESESABLE_NH_CHARS_PATTERN = Pattern.compile( "[(),;\\s:\\[\\]]" ); static { final DecimalFormatSymbols dfs = new DecimalFormatSymbols(); @@ -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; } } @@ -594,6 +595,13 @@ public final class ForesterUtil { return ( ( s == null ) || ( s.length() < 1 ) ); } + final public static boolean isEmptyTrimmed( final String s ) { + if ( s == null ) { + return true; + } + return ( ( s.trim().length() < 1 ) ); + } + /** * Returns true is Domain domain falls in an uninterrupted stretch of * covered positions. @@ -615,6 +623,10 @@ public final class ForesterUtil { return ( ( Math.abs( a - b ) ) < ZERO_DIFF ); } + final public static boolean isEqual( final double a, final double b, final double tolerance ) { + return ( ( Math.abs( a - b ) ) < tolerance ); + } + final public static boolean isEven( final int n ) { return ( n % 2 ) == 0; } @@ -712,6 +724,10 @@ public final class ForesterUtil { return null; } + final public static String isWritableFile( final String s ) { + return isWritableFile( new File( s ) ); + } + /** * Helper for method "stringToColor". *
@@ -1502,7 +1518,7 @@ public final class ForesterUtil {
is.close();
}
catch ( final Exception e ) {
- // ignore
+ // ignore
}
return trees;
}
@@ -1534,7 +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 ) {
@@ -1572,6 +1588,123 @@ public final class ForesterUtil {
return the_one;
}
+ public final static String greatestCommonPrefix( final String a, final String b ) {
+ final int min_length = Math.min( a.length(), b.length() );
+ for( int i = 0; i < min_length; ++i ) {
+ if ( a.charAt( i ) != b.charAt( i ) ) {
+ return a.substring( 0, i );
+ }
+ }
+ 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" );
+ }
+ final String[] as = a.split( Pattern.quote( separator ) );
+ final String[] bs = b.split( Pattern.quote( separator ) );
+ final int min_length = Math.min( as.length, bs.length );
+ for( int i = 0; i < min_length; ++i ) {
+ if ( !( as[ i ].equals( bs[ i ] ) ) ) {
+ final StringBuilder sb = new StringBuilder();
+ boolean first = true;
+ for( int j = 0; j < i; ++j ) {
+ if ( first ) {
+ first = false;
+ }
+ else {
+ sb.append( separator );
+ }
+ sb.append( as[ j ] );
+ }
+ return sb.toString();
+ }
+ }
+ final StringBuilder sb = new StringBuilder();
+ boolean first = true;
+ for( int j = 0; j < min_length; ++j ) {
+ if ( first ) {
+ first = false;
+ }
+ else {
+ sb.append( separator );
+ }
+ sb.append( as[ j ] );
+ }
+ return sb.toString();
+ }
+
+ public final static String greatestCommonPrefix( final List