X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Futil%2FForesterUtil.java;h=336c88763124454613da3df163c1535e93f9810a;hb=bc282cbd857f4fb9decdc00b278640bcf146a645;hp=58dbf453bb55a9af5823952e689569056a8df3ea;hpb=3be5f9e46469980f068a9f8170e1d20849b5eaf8;p=jalview.git

diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java
index 58dbf45..336c887 100644
--- a/forester/java/src/org/forester/util/ForesterUtil.java
+++ b/forester/java/src/org/forester/util/ForesterUtil.java
@@ -61,6 +61,11 @@ import java.util.TreeMap;
 import java.util.TreeSet;
 import java.util.regex.Pattern;
 
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Distribution;
+import org.forester.phylogeny.data.Sequence;
+import org.forester.phylogeny.data.Taxonomy;
+
 public final class ForesterUtil {
 
     public final static String       FILE_SEPARATOR                   = System.getProperty( "file.separator" );
@@ -90,12 +95,44 @@ public final class ForesterUtil {
     private ForesterUtil() {
     }
 
+    public static void ensurePresenceOfTaxonomy( final PhylogenyNode node ) {
+        if ( !node.getNodeData().isHasTaxonomy() ) {
+            node.getNodeData().setTaxonomy( new Taxonomy() );
+        }
+    }
+
+    public static void ensurePresenceOfSequence( final PhylogenyNode node ) {
+        if ( !node.getNodeData().isHasSequence() ) {
+            node.getNodeData().setSequence( new Sequence() );
+        }
+    }
+
+    final public static void ensurePresenceOfDistribution( final PhylogenyNode node ) {
+        if ( !node.getNodeData().isHasDistribution() ) {
+            node.getNodeData().setDistribution( new Distribution( "" ) );
+        }
+    }
+
+    final public static void ensurePresenceOfDate( final PhylogenyNode node ) {
+        if ( !node.getNodeData().isHasDate() ) {
+            node.getNodeData().setDate( new org.forester.phylogeny.data.Date() );
+        }
+    }
+
     final public static void appendSeparatorIfNotEmpty( final StringBuffer sb, final char separator ) {
         if ( sb.length() > 0 ) {
             sb.append( separator );
         }
     }
 
+    public static boolean isWindowns() {
+        return ForesterUtil.OS_NAME.toLowerCase().indexOf( "win" ) > -1;
+    }
+
+    final public static String getForesterLibraryInformation() {
+        return "forester " + ForesterConstants.FORESTER_VERSION + " (" + ForesterConstants.FORESTER_DATE + ")";
+    }
+
     public static boolean seqIsLikelyToBeAa( final String s ) {
         final String seq = s.toLowerCase();
         if ( ( seq.indexOf( 'r' ) > -1 ) || ( seq.indexOf( 'd' ) > -1 ) || ( seq.indexOf( 'e' ) > -1 )
@@ -300,6 +337,14 @@ public final class ForesterUtil {
         return new BufferedWriter( new FileWriter( file ) );
     }
 
+    final public static EasyWriter createEasyWriter( final File file ) throws IOException {
+        return new EasyWriter( createBufferedWriter( file ) );
+    }
+
+    final public static BufferedWriter createEasyWriter( final String name ) throws IOException {
+        return createEasyWriter( createFileForWriting( name ) );
+    }
+
     final public static BufferedWriter createBufferedWriter( final String name ) throws IOException {
         return new BufferedWriter( new FileWriter( createFileForWriting( name ) ) );
     }
@@ -319,6 +364,16 @@ public final class ForesterUtil {
         System.exit( -1 );
     }
 
+    public static void fatalErrorIfFileNotReadable( final String prg_name, final File file ) {
+        final String error = isReadableFile( file );
+        if ( !isEmpty( error ) ) {
+            System.err.println();
+            System.err.println( "[" + prg_name + "] > " + error );
+            System.err.println();
+            System.exit( -1 );
+        }
+    }
+
     public static String[] file2array( final File file ) throws IOException {
         final List<String> list = file2list( file );
         final String[] ary = new String[ list.size() ];
@@ -466,7 +521,7 @@ public final class ForesterUtil {
     }
 
     final public static boolean isEven( final int n ) {
-        return n % 2 == 0;
+        return ( n % 2 ) == 0;
     }
 
     /**
@@ -486,10 +541,9 @@ public final class ForesterUtil {
         if ( ( a.length < 1 ) || ( b.length < 1 ) ) {
             return false;
         }
-        for( int i = 0; i < a.length; ++i ) {
-            final String ai = a[ i ];
-            for( int j = 0; j < b.length; ++j ) {
-                if ( ( ai != null ) && ( b[ j ] != null ) && ai.equals( b[ j ] ) ) {
+        for( final String ai : a ) {
+            for( final String element : b ) {
+                if ( ( ai != null ) && ( element != null ) && ai.equals( element ) ) {
                     return true;
                 }
             }
@@ -717,7 +771,7 @@ public final class ForesterUtil {
     }
 
     final public static void printErrorMessage( final String prg_name, final String message ) {
-        System.out.println( "[" + prg_name + "] > error: " + message );
+        System.err.println( "[" + prg_name + "] > error: " + message );
     }
 
     final public static void printProgramInformation( final String prg_name, final String prg_version, final String date ) {
@@ -731,20 +785,29 @@ public final class ForesterUtil {
     }
 
     final public static void printProgramInformation( final String prg_name,
+                                                      final String desc,
                                                       final String prg_version,
                                                       final String date,
                                                       final String email,
-                                                      final String www ) {
-        final int l = prg_name.length() + prg_version.length() + date.length() + 4;
+                                                      final String www,
+                                                      final String based_on ) {
+        String my_prg_name = new String( prg_name );
+        if ( !ForesterUtil.isEmpty( desc ) ) {
+            my_prg_name += ( " - " + desc );
+        }
+        final int l = my_prg_name.length() + prg_version.length() + date.length() + 4;
         System.out.println();
-        System.out.println( prg_name + " " + prg_version + " (" + date + ")" );
+        System.out.println( my_prg_name + " " + prg_version + " (" + date + ")" );
         for( int i = 0; i < l; ++i ) {
             System.out.print( "_" );
         }
         System.out.println();
         System.out.println();
-        System.out.println( "WWW    : " + www );
-        System.out.println( "Contact: " + email );
+        System.out.println( "WWW     : " + www );
+        System.out.println( "Contact : " + email );
+        if ( !ForesterUtil.isEmpty( based_on ) ) {
+            System.out.println( "Based on: " + based_on );
+        }
         if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
             System.out.println();
             System.out.println( "[running on Java " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
@@ -752,6 +815,14 @@ public final class ForesterUtil {
         System.out.println();
     }
 
+    final public static void printProgramInformation( final String prg_name,
+                                                      final String prg_version,
+                                                      final String date,
+                                                      final String email,
+                                                      final String www ) {
+        printProgramInformation( prg_name, null, prg_version, date, email, www, null );
+    }
+
     final public static void printWarningMessage( final String prg_name, final String message ) {
         System.out.println( "[" + prg_name + "] > warning: " + message );
     }
@@ -775,7 +846,7 @@ public final class ForesterUtil {
      */
     final public static String removeWhiteSpace( String s ) {
         int i;
-        for( i = 0; i <= s.length() - 1; i++ ) {
+        for( i = 0; i <= ( s.length() - 1 ); i++ ) {
             if ( ( s.charAt( i ) == ' ' ) || ( s.charAt( i ) == '\t' ) || ( s.charAt( i ) == '\n' )
                     || ( s.charAt( i ) == '\r' ) ) {
                 s = s.substring( 0, i ) + s.substring( i + 1 );
@@ -841,7 +912,7 @@ public final class ForesterUtil {
     final public static String stringArrayToString( final String[] a, final String separator ) {
         final StringBuilder sb = new StringBuilder();
         if ( ( a != null ) && ( a.length > 0 ) ) {
-            for( int i = 0; i < a.length - 1; ++i ) {
+            for( int i = 0; i < ( a.length - 1 ); ++i ) {
                 sb.append( a[ i ] + separator );
             }
             sb.append( a[ a.length - 1 ] );
@@ -864,7 +935,7 @@ public final class ForesterUtil {
     final public static String stringListToString( final List<String> l, final String separator ) {
         final StringBuilder sb = new StringBuilder();
         if ( ( l != null ) && ( l.size() > 0 ) ) {
-            for( int i = 0; i < l.size() - 1; ++i ) {
+            for( int i = 0; i < ( l.size() - 1 ); ++i ) {
                 sb.append( l.get( i ) + separator );
             }
             sb.append( l.get( l.size() - 1 ) );
@@ -884,7 +955,7 @@ public final class ForesterUtil {
     final public static void unexpectedFatalError( final String prg_name, final Exception e ) {
         System.err.println();
         System.err.println( "[" + prg_name
-                + "] > unexpected error (Should not have occured! Please contact program author(s).)" );
+                + "] > Unexpected error. Should not have occured! Please contact program author(s)." );
         e.printStackTrace( System.err );
         System.err.println();
         System.exit( -1 );
@@ -893,7 +964,7 @@ public final class ForesterUtil {
     final public static void unexpectedFatalError( final String prg_name, final String message ) {
         System.err.println();
         System.err.println( "[" + prg_name
-                + "] > unexpected error. Should not have occured! Please contact program author(s)." );
+                + "] > Unexpected error. Should not have occured! Please contact program author(s)." );
         System.err.println( message );
         System.err.println();
         System.exit( -1 );
@@ -902,7 +973,7 @@ public final class ForesterUtil {
     final public static void unexpectedFatalError( final String prg_name, final String message, final Exception e ) {
         System.err.println();
         System.err.println( "[" + prg_name
-                + "] > unexpected error. Should not have occured! Please contact program author(s)." );
+                + "] > Unexpected error. Should not have occured! Please contact program author(s)." );
         System.err.println( message );
         e.printStackTrace( System.err );
         System.err.println();
@@ -922,7 +993,7 @@ public final class ForesterUtil {
                 ls = -1;
                 start = i + 1;
             }
-            if ( i > start + width - 1 ) {
+            if ( i > ( ( start + width ) - 1 ) ) {
                 if ( ls != -1 ) {
                     sb.setCharAt( ls, '\n' );
                     start = ls + 1;