in progress

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/ImageLoader.java b/forester/java/src/org/forester/archaeopteryx/tools/ImageLoader.java
index 777dacf..b81cc25 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/ImageLoader.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/ImageLoader.java
@@ -46,6 +46,7 @@ public class ImageLoader implements Runnable {
 
     private final TreePanel            _tp;
     private static final BufferedImage PLACEHOLDER = new BufferedImage( 1, 1, BufferedImage.TYPE_INT_RGB );
+    private final static boolean       DEBUG       = false;
 
     public ImageLoader( final TreePanel tp ) {
         _tp = tp;
@@ -82,8 +83,8 @@ public class ImageLoader implements Runnable {
                                         || uri_str.endsWith( ".gif" ) || uri_str.endsWith( ".bmp" ) ) ) {
                             image_map.put( uri_str, PLACEHOLDER );
                             BufferedImage bi = null;
-                            if ( !Constants.__RELEASE && !Constants.__SNAPSHOT_RELEASE ) {
-                                System.out.println( "accessing:" + uri );
+                            if ( DEBUG ) {
+                                System.out.println( "accessing: " + uri );
                             }
                             try {
                                 bi = ImageIO.read( uri.getValue().toURL() );

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
index 1d8309f..fea0bd5 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
@@ -226,7 +226,7 @@ public class PhylogeneticInferrer implements Runnable {
         try {
             infer();
         }
-        catch ( InterruptedException e ) {
+        catch ( final InterruptedException e ) {
             // TODO need to handle this exception SOMEHOW!
             // TODO Auto-generated catch block
             e.printStackTrace();

diff --git a/forester/java/src/org/forester/go/BasicGoSubset.java b/forester/java/src/org/forester/go/BasicGoSubset.java
index dc63b52..82015fb 100644 (file)
--- a/forester/java/src/org/forester/go/BasicGoSubset.java
+++ b/forester/java/src/org/forester/go/BasicGoSubset.java
@@ -46,6 +46,9 @@ public class BasicGoSubset implements GoSubset {
         else if ( my_s.equals( GOSLIM_CANDIDA_STR ) ) {
             _type = Type.GOSLIM_CANDIDA;
         }
+        else if ( my_s.equals( GOSLIM_ASPERGILLUS_STR ) ) {
+            _type = Type.GOSLIM_ASPERGILLUS;
+        }
         else if ( my_s.equals( GOSLIM_PLANT_STR ) ) {
             _type = Type.GOSLIM_PLANT;
         }
@@ -61,6 +64,9 @@ public class BasicGoSubset implements GoSubset {
         else if ( my_s.equals( UNVETTED_STR ) ) {
             _type = Type.UNVETTED;
         }
+        else if ( my_s.equals( MF_NEEDS_REVIEW_STR ) ) {
+            _type = Type.MF_NEEDS_REVIEW;
+        }
         else {
             throw new IllegalArgumentException( "unknown GO subset type: " + my_s );
         }
@@ -116,6 +122,9 @@ public class BasicGoSubset implements GoSubset {
             case GOSLIM_PLANT:
                 sb.append( GOSLIM_PLANT_STR );
                 break;
+            case GOSLIM_ASPERGILLUS:
+                sb.append( GOSLIM_ASPERGILLUS_STR );
+                break;
             case GOSLIM_YEAST:
                 sb.append( GOSLIM_YEAST_STR );
                 break;
@@ -125,6 +134,15 @@ public class BasicGoSubset implements GoSubset {
             case GOSLIM_POMBE:
                 sb.append( GOSLIM_POMBE_STR );
                 break;
+            case MF_NEEDS_REVIEW:
+                sb.append( MF_NEEDS_REVIEW_STR );
+                break;
+            case HIGH_LEVEL_ANNOTATION_QC:
+                sb.append( HIGH_LEVEL_ANNOTATION_QC_STR );
+                break;
+            case UNVETTED:
+                sb.append( UNVETTED_STR );
+                break;
             default:
                 new AssertionError( "unknown type: " + getType() );
         }

diff --git a/forester/java/src/org/forester/go/GoSubset.java b/forester/java/src/org/forester/go/GoSubset.java
index 64773d0..1ee494c 100644 (file)
--- a/forester/java/src/org/forester/go/GoSubset.java
+++ b/forester/java/src/org/forester/go/GoSubset.java
@@ -32,11 +32,13 @@ public interface GoSubset extends Comparable<GoSubset> {
     public static final String GOSLIM_PIR_STR               = "goslim_pir";
     public static final String GOSUBSET_PROK_STR            = "gosubset_prok";
     public static final String GOSLIM_CANDIDA_STR           = "goslim_candida";
+    public static final String GOSLIM_ASPERGILLUS_STR       = "goslim_aspergillus";
     public static final String GOSLIM_PLANT_STR             = "goslim_plant";
     public static final String GOSLIM_YEAST_STR             = "goslim_yeast";
     public static final String GOSLIM_POMBE_STR             = "goslim_pombe";
     public static final String HIGH_LEVEL_ANNOTATION_QC_STR = "high_level_annotation_qc";
     public static final String UNVETTED_STR                 = "unvetted";
+    public static final String MF_NEEDS_REVIEW_STR          = "mf_needs_review";
 
     public Type getType();
 
@@ -46,10 +48,12 @@ public interface GoSubset extends Comparable<GoSubset> {
         GOSLIM_PIR,
         GOSUBSET_PROK,
         GOSLIM_CANDIDA,
+        GOSLIM_ASPERGILLUS,
         GOSLIM_PLANT,
         GOSLIM_YEAST,
         GOSLIM_POMBE,
         HIGH_LEVEL_ANNOTATION_QC,
-        UNVETTED;
+        UNVETTED,
+        MF_NEEDS_REVIEW;
     }
 }

diff --git a/forester/java/src/org/forester/msa/Mafft.java b/forester/java/src/org/forester/msa/Mafft.java
index 81e43b2..0cdaac2 100644 (file)
--- a/forester/java/src/org/forester/msa/Mafft.java
+++ b/forester/java/src/org/forester/msa/Mafft.java
@@ -114,7 +114,7 @@ public final class Mafft implements MsaInferrer {
         }
         final StringBuilder stdout = command_executor.getStandardOutputFromCommand();
         final StringBuilder stderr = command_executor.getStandardErrorFromCommand();
-        if ( stdout == null || stdout.length() < 2 ) {
+        if ( ( stdout == null ) || ( stdout.length() < 2 ) ) {
             throw new IOException( "MAFFT program did not produce any output, command: " + my_opts );
         }
         _error = stderr.toString();

diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
index 2a607cd..3a9d10e 100644 (file)
--- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java
+++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
@@ -673,7 +673,7 @@ public final class SurfacingUtil {
                 randomization = "yes, seed = " + random_number_seed_for_fitch_parsimony;
             }
             else {
-                domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( false );
+                domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( true );
             }
             SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
                     + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );