in progress

[jalview.git] / forester / java / src / org / forester / archaeopteryx / AptxUtil.java

diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index 21a4ace..cc0c365 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@ -50,6 +50,8 @@ import java.util.Map;
 import java.util.Set;
 import java.util.SortedSet;
 import java.util.TreeSet;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 import javax.imageio.IIOImage;
 import javax.imageio.ImageIO;
@@ -68,6 +70,7 @@ import org.forester.io.parsers.util.ParserUtils;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Accession;
 import org.forester.phylogeny.data.BranchColor;
 import org.forester.phylogeny.data.Distribution;
 import org.forester.phylogeny.data.Sequence;
@@ -82,12 +85,38 @@ import org.forester.ws.uniprot.UniProtTaxonomy;
 
 public final class AptxUtil {
 
+    private final static Pattern  seq_identifier_pattern_1       = Pattern
+                                                                         .compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z_\\.]{5,40})\\s*$" );
+    private final static Pattern  seq_identifier_pattern_2       = Pattern
+                                                                         .compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z_\\.]{5,40})[|,; ].*$" );
     private final static String[] AVAILABLE_FONT_FAMILIES_SORTED = GraphicsEnvironment.getLocalGraphicsEnvironment()
                                                                          .getAvailableFontFamilyNames();
     static {
         Arrays.sort( AVAILABLE_FONT_FAMILIES_SORTED );
     }
 
+    public final static Accession obtainSequenceAccessionFromName( final String sequence_name ) {
+        final String n = sequence_name.trim();
+        final Matcher matcher1 = seq_identifier_pattern_1.matcher( n );
+        String group1 = "";
+        String group2 = "";
+        if ( matcher1.matches() ) {
+            group1 = matcher1.group( 1 );
+            group2 = matcher1.group( 2 );
+        }
+        else {
+            final Matcher matcher2 = seq_identifier_pattern_2.matcher( n );
+            if ( matcher2.matches() ) {
+                group1 = matcher2.group( 1 );
+                group2 = matcher2.group( 2 );
+            }
+        }
+        if ( ForesterUtil.isEmpty( group1 ) || ForesterUtil.isEmpty( group2 ) ) {
+            return null;
+        }
+        return new Accession( group2, group1 );
+    }
+
     public static void ensurePresenceOfTaxonomy( final PhylogenyNode node ) {
         if ( !node.getNodeData().isHasTaxonomy() ) {
             node.getNodeData().setTaxonomy( new Taxonomy() );
@@ -131,6 +160,17 @@ public final class AptxUtil {
         final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType( intree, true );
         Phylogeny[] phys = null;
         phys = PhylogenyMethods.readPhylogenies( parser, intree );
+        writePhylogenyToGraphicsFile( phys[ 0 ], outfile, width, height, type, config );
+    }
+
+    public static void writePhylogenyToGraphicsFile( final Phylogeny phy,
+                                                     final File outfile,
+                                                     final int width,
+                                                     final int height,
+                                                     final GraphicsExportType type,
+                                                     final Configuration config ) throws IOException {
+        final Phylogeny[] phys = new Phylogeny[ 1 ];
+        phys[ 0 ] = phy;
         final MainFrameApplication mf = MainFrameApplication.createInstance( phys, config );
         AptxUtil.writePhylogenyToGraphicsFileNonInteractive( outfile, width, height, mf.getMainPanel()
                 .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() );
@@ -667,10 +707,10 @@ public final class AptxUtil {
         }
     }
 
-    final static void launchWebBrowser( final URI uri,
-                                        final boolean is_applet,
-                                        final JApplet applet,
-                                        final String frame_name ) throws IOException {
+    final public static void launchWebBrowser( final URI uri,
+                                               final boolean is_applet,
+                                               final JApplet applet,
+                                               final String frame_name ) throws IOException {
         if ( is_applet ) {
             applet.getAppletContext().showDocument( uri.toURL(), frame_name );
         }
@@ -824,7 +864,7 @@ public final class AptxUtil {
         }
     }
 
-    final static void showErrorMessage( final Component parent, final String error_msg ) {
+    final public static void showErrorMessage( final Component parent, final String error_msg ) {
         printAppletMessage( Constants.PRG_NAME, error_msg );
         JOptionPane.showMessageDialog( parent, error_msg, "[" + Constants.PRG_NAME + " " + Constants.VERSION
                 + "] Error", JOptionPane.ERROR_MESSAGE );