From: cmzmasek@gmail.com Date: Wed, 8 Feb 2012 21:14:37 +0000 (+0000) Subject: in progress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=fbba20dcd57f706d5bf42c4f3f157e053a24cc97;p=jalview.git 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 --- 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 --- 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 --- 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 --- 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 { 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 { 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 --- 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 --- 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 );