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sigmarkarl · Feb 23, 2017 · ae0c508 · ae0c508
1 parent 3ff685b
commit ae0c508
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Showing 2 changed files with 32 additions and 15 deletions.
diff --git a/distann/src/main/java/org/simmi/GeneSet.java b/distann/src/main/java/org/simmi/GeneSet.java
@@ -491,7 +491,7 @@ private void loci2aaseq( List<Set<String>> lclust, Map<String,Gene> refmap, Map<
 					u = Sequence.specCheck( contigstr );
 
 					if( u == -1 ) {
-						u = Serifier.contigIndex( contigstr );
+						u = Sequence.parseSpec( contigstr );
 						if( u > 0 ) {
 							origin = contigstr.substring(0, u - 1);
 							contloc = contigstr.substring(u, contigstr.length());
@@ -707,10 +707,6 @@ private void loci2aaseq( List<Set<String>> lclust, Map<String,Gene> refmap, Map<
 
 	Set<String>	mu = new HashSet<>();
 	private void loci2aasequence(BufferedReader br, Map<String,Gene> refmap, Map<String,String> designations, String filename) throws IOException {
-		/*if( filename.contains("timi") ) {
-			System.err.println();
-		}*/
-
 		String line = br.readLine();
 		String lname = null;
 		String prevline = null;
@@ -742,6 +738,7 @@ private void loci2aasequence(BufferedReader br, Map<String,Gene> refmap, Map<Str
 
 						if( i == 0 ) {
 							int k = filename.indexOf('_');
+							if( k == -1 ) k = filename.indexOf('.');
 							if( k == -1 ) k = filename.length();
 							origin = filename.substring(0, k);
 							contloc = lname;
@@ -777,7 +774,7 @@ private void loci2aasequence(BufferedReader br, Map<String,Gene> refmap, Map<Str
 							/*u = contigstr.indexOf("contig");
 							if( u == -1 ) u = contigstr.indexOf("scaffold");
 							if( u == -1 ) u = contigstr.lastIndexOf('_')+1;*/
-							u = Serifier.contigIndex( contigstr );
+							u = Sequence.parseSpec( contigstr );
 							if( u == 0 ) {
 								System.err.println();
 							}
@@ -1062,7 +1059,7 @@ private void loci2aasequence(BufferedReader br, Map<String,Gene> refmap, Map<Str
 				u = Sequence.specCheck( contigstr );
 
 				if( u == -1 ) {
-					u = Serifier.contigIndex( contigstr );
+					u = Sequence.parseSpec( contigstr );
 					/*u = contigstr.indexOf("contig");
 					if( u == -1 ) u = contigstr.indexOf("scaffold");
 					if( u == -1 ) u = contigstr.lastIndexOf('_')+1;*/
@@ -1178,8 +1175,18 @@ private List<String> loadcontigs(BufferedReader br, String filename) throws IOEx
 			if (line.startsWith(">")) {
 				if( size > 0 ) {
 					Sequence contig = new Contig( name, ac );
-					
+
 					String spec = contig.getSpec();
+					if( spec == null ) {
+						spec = Contig.getSpec( name );
+						if( spec == null ) {
+							int di = filename.indexOf('_');
+							if (di == -1) di = filename.indexOf('.');
+							if (di == -1) di = filename.length();
+							spec = filename.substring(0, di);
+						}
+						contig.setGroup(spec);
+					}
 					List<Sequence>	ctlist;
 					if( speccontigMap.containsKey( spec ) ) {
 						ctlist = speccontigMap.get( spec );
@@ -1231,6 +1238,16 @@ private List<String> loadcontigs(BufferedReader br, String filename) throws IOEx
 
 			List<Sequence>	ctlist;
 			String spec = contig.getSpec();
+			if( spec == null ) {
+				spec = Contig.getSpec( name );
+				if( spec == null ) {
+					int di = filename.indexOf('_');
+					if (di == -1) di = filename.indexOf('.');
+					if (di == -1) di = filename.length();
+					spec = filename.substring(0, di);
+				}
+				contig.setGroup(spec);
+			}
 
 			if( speccontigMap.containsKey( spec ) ) {
 				ctlist = speccontigMap.get( spec );
@@ -6790,7 +6807,7 @@ public Serifier getConcatenatedSequences( boolean proximityJoin, Map<GeneGroup,I
 						}
 						seqs.putAll( addseqs );
 					} else {
-						seqs = new HashMap<Sequence,String>();
+						seqs = new HashMap<>();
 
 						if( ltv != null && ltv.size() > 0 ) {
 							for( Tegeval tv : ltv ) {
@@ -6830,14 +6847,14 @@ public Serifier getConcatenatedSequences( boolean proximityJoin, Map<GeneGroup,I
 					if( donetvs.containsKey(spec) ) {
 						tvals = donetvs.get( spec );
 					} else {
-						tvals = new HashSet<Tegeval>();
+						tvals = new HashSet<>();
 						donetvs.put( spec, tvals );
 					}
 
 					if( smap.containsKey( spec ) ) {
 						seqs = smap.get( spec );
-						Map<Sequence,String> 	addseqs = new HashMap<Sequence,String>();
-						Set<Tegeval>			accountedfor = new HashSet<Tegeval>();
+						Map<Sequence,String> 	addseqs = new HashMap<>();
+						Set<Tegeval>			accountedfor = new HashSet<>();
 
 						for( Sequence seq : seqs.keySet() ) {
 							String loc = seqs.get( seq );
@@ -7052,7 +7069,7 @@ public void cogCalc( String filename, BufferedReader br, Map<String,Map<Characte
 									else name = "Thermus_" + nspec.substring(0,firstDigitLocation) + "_" + nspec.substring(firstDigitLocation);
 								}*/
 
-								int k = Serifier.contigIndex(name);
+								int k = Sequence.parseSpec(name);
 								if( k == -1 ) {
 									name = spec;
 								} else {
@@ -7563,7 +7580,7 @@ public int loadrnas( Map<String,GeneGroup>	ggmap, Reader reader, int groupIndex,
 				int u = Sequence.specCheck( cont );
 
 				if( u == -1 ) {
-					u = Serifier.contigIndex(cont);
+					u = Sequence.parseSpec(cont);
 					spec = cont.substring( 0, u-1 );
 					contshort = cont.substring( u, cont.length() );
 				} else {

diff --git a/serifier/src/main/java/org/simmi/SerifyApplet.java b/serifier/src/main/java/org/simmi/SerifyApplet.java
@@ -5045,7 +5045,7 @@ public void addSequences( String name, Map<String,Reader> rds, Path path, String
 								nseq++;
 
 								if( nseq % 1000 == 0 ) System.err.println( "seq counting: "+nseq );
-							} else if( type.equals("nucl") && !line.matches("^[acgtykvrswmunxACGTDYKVRSWMUNX]+$") ) {
+							} else if( type.equals("nucl") && line.length() > 0 && !line.matches("^[acgtbdykhvrswmunxACGTBDYKHVRSWMUNX]+$") ) {
 								type = "prot";
 							}
 							line = br.readLine();