X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FAptxUtil.java;h=b2c3dd849557588b203a4ed4be00d75f721d877f;hb=362bd0a813f302f28631d9c9447dd8aa9ee0ceda;hp=c56d068e4b35d2a3fe56545a97ce745f5b6f586f;hpb=ff79eee1cd2e65925ada2e6fd484010122c74d22;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index c56d068..b2c3dd8 100644
--- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@ -25,6 +25,7 @@
 
 package org.forester.archaeopteryx;
 
+import java.awt.Color;
 import java.awt.Component;
 import java.awt.Graphics2D;
 import java.awt.GraphicsEnvironment;
@@ -40,6 +41,7 @@ import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Method;
 import java.net.URI;
 import java.net.URL;
+import java.net.URLConnection;
 import java.text.ParseException;
 import java.util.Arrays;
 import java.util.HashSet;
@@ -70,6 +72,7 @@ import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
 import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Confidence;
 import org.forester.phylogeny.data.Taxonomy;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
 import org.forester.phylogeny.factories.PhylogenyFactory;
@@ -133,6 +136,46 @@ public final class AptxUtil {
         return false;
     }
 
+    final static public boolean isHasAtLeastOneBranchWithSupportSD( final Phylogeny phy ) {
+        final PhylogenyNodeIterator it = phy.iteratorPostorder();
+        while ( it.hasNext() ) {
+            final PhylogenyNode n = it.next();
+            if ( n.getBranchData().isHasConfidences() ) {
+                final List<Confidence> c = n.getBranchData().getConfidences();
+                for( final Confidence confidence : c ) {
+                    if ( confidence.getStandardDeviation() > 0 ) {
+                        return true;
+                    }
+                }
+            }
+        }
+        return false;
+    }
+
+    final static public boolean isHasAtLeastOneNodeWithScientificName( final Phylogeny phy ) {
+        final PhylogenyNodeIterator it = phy.iteratorPostorder();
+        while ( it.hasNext() ) {
+            final PhylogenyNode n = it.next();
+            if ( n.getNodeData().isHasTaxonomy()
+                    && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+                return true;
+            }
+        }
+        return false;
+    }
+
+    final static public boolean isHasAtLeastOneNodeWithSequenceAnnotation( final Phylogeny phy ) {
+        final PhylogenyNodeIterator it = phy.iteratorPostorder();
+        while ( it.hasNext() ) {
+            final PhylogenyNode n = it.next();
+            if ( n.getNodeData().isHasSequence()
+                    && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAnnotations() ) ) {
+                return true;
+            }
+        }
+        return false;
+    }
+
     final public static void launchWebBrowser( final URI uri,
                                                final boolean is_applet,
                                                final JApplet applet,
@@ -680,7 +723,9 @@ public final class AptxUtil {
             }
         }
         AptxUtil.printAppletMessage( "Archaeopteryx", "parser is " + parser.getName() );
-        final InputStream i = url.openStream();
+        final URLConnection url_connection = url.openConnection();
+        url_connection.setDefaultUseCaches( false );
+        final InputStream i = url_connection.getInputStream();
         final Phylogeny[] phys = factory.create( i, parser );
         i.close();
         if ( phys != null ) {
@@ -943,30 +988,6 @@ public final class AptxUtil {
         }
     }
 
-    // See: http://www.xml.nig.ac.jp/tutorial/rest/index.html#2.2
-    // static void openDDBJRest() throws IOException {
-    // //set URL
-    // URL url = new URL( "http://xml.nig.ac.jp/rest/Invoke" );
-    // //set parameter
-    // String query = "service=GetEntry&method=getDDBJEntry&accession=AB000100";
-    // //make connection
-    // URLConnection urlc = url.openConnection();
-    // //use post mode
-    // urlc.setDoOutput( true );
-    // urlc.setAllowUserInteraction( false );
-    // //send query
-    // PrintStream ps = new PrintStream( urlc.getOutputStream() );
-    // ps.print( query );
-    // ps.close();
-    // //get result
-    // BufferedReader br = new BufferedReader( new InputStreamReader(
-    // urlc.getInputStream() ) );
-    // String l = null;
-    // while ( ( l = br.readLine() ) != null ) {
-    // System.out.println( l );
-    // }
-    // br.close();
-    // }
     public static enum GraphicsExportType {
         BMP( "bmp" ), GIF( "gif" ), JPG( "jpg" ), PDF( "pdf" ), PNG( "png" ), TIFF( "tif" );
 
@@ -981,4 +1002,50 @@ public final class AptxUtil {
             return _suffix;
         }
     }
+
+    final public static Color calculateColorFromString( final String str, final boolean is_taxonomy ) {
+        final String my_str = str.toUpperCase();
+        char first = my_str.charAt( 0 );
+        char second = ' ';
+        char third = ' ';
+        if ( my_str.length() > 1 ) {
+            if ( is_taxonomy ) {
+                second = my_str.charAt( 1 );
+            }
+            else {
+                second = my_str.charAt( my_str.length() - 1 );
+            }
+            if ( is_taxonomy ) {
+                if ( my_str.length() > 2 ) {
+                    if ( my_str.indexOf( " " ) > 0 ) {
+                        third = my_str.charAt( my_str.indexOf( " " ) + 1 );
+                    }
+                    else {
+                        third = my_str.charAt( 2 );
+                    }
+                }
+            }
+            else if ( my_str.length() > 2 ) {
+                third = my_str.charAt( ( my_str.length() - 1 ) / 2 );
+            }
+        }
+        first = normalizeCharForRGB( first );
+        second = normalizeCharForRGB( second );
+        third = normalizeCharForRGB( third );
+        if ( ( first > 235 ) && ( second > 235 ) && ( third > 235 ) ) {
+            first = 0;
+        }
+        else if ( ( first < 60 ) && ( second < 60 ) && ( third < 60 ) ) {
+            second = 255;
+        }
+        return new Color( first, second, third );
+    }
+
+    final private static char normalizeCharForRGB( char c ) {
+        c -= 65;
+        c *= 10.2;
+        c = c > 255 ? 255 : c;
+        c = c < 0 ? 0 : c;
+        return c;
+    }
 }