Merge branch 'master' of github.com:andreasprlic/biojava

andreasprlic · andreasprlic · commit 388220da1659 · 2016-07-25T22:04:12.000-07:00
* 'master' of github.com:andreasprlic/biojava:
  updating icon to new official BioJava logo
  adding tools to map from chromosome positions to mRNA coding sequence position.

# Conflicts:
#	biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java
@@ -20,6 +20,7 @@ public class ChromosomeMappingTools {
     public static final boolean debug = false;
     private static final String newline = System.getProperty("line.separator");
 
+
     public static final String CHROMOSOME = "CHROMOSOME";
     public static final String CDS = "CDS";
 
@@ -36,6 +37,7 @@ public static String printHTMLExonStructure(GeneChromosomePosition chromosomePos
             return printHTMLExonStructureForward(chromosomePosition);
 
         return printHTMLExonStructureReverse(chromosomePosition);
+
     }
 
     private static String formatExonStructureForward(GeneChromosomePosition chromPos) {
@@ -765,8 +767,10 @@ public static int getCDSLengthReverse(List<Integer> exonStarts,
                 inCoding = false;
                 codingLength += (end - cdsStart);
                 if (debug) {
+
                     System.out.println(" <-  Exon        : " + (cdsStart+1) + " - " + end + " | " + (end - cdsStart) + " | " + (codingLength-3)  + " | " + (codingLength % 3));
                     System.out.println("     UTR         : " + start + " - " + (cdsStart ));
+
                 }
 
             } else if (inCoding) {
@@ -863,6 +867,7 @@ public static int getCDSLengthForward(List<Integer> exonStarts, List<Integer> ex
      */
     public static List<Range> getCDSExonRanges(GeneChromosomePosition chromPos){
         if ( chromPos.getOrientation() == '+')
+
             return getCDSExonRangesForward(chromPos,CDS);
 
         return getCDSExonRangesReverse(chromPos,CDS);
@@ -883,6 +888,7 @@ public static List<Range> getChromosomalRangesForCDS(GeneChromosomePosition chro
 
     private static List<Range> getCDSExonRangesReverse(GeneChromosomePosition chromPos,
                                                        String responseType) {
+
         List<Integer> exonStarts = chromPos.getExonStarts();
         List<Integer> exonEnds   = chromPos.getExonEnds();
 
@@ -944,6 +950,7 @@ private static List<Range> getCDSExonRangesReverse(GeneChromosomePosition chromP
                     s.append(newline);
                 }
 
+
                 Range r ;
                 if ( responseType.equals(CDS))
                     r = Range.closed(0,codingLength);
@@ -954,6 +961,7 @@ private static List<Range> getCDSExonRangesReverse(GeneChromosomePosition chromP
 
             } else if (start <= cdsStart && end >= cdsStart) {
                 inCoding = false;
+
                 Range r;
                 if ( responseType.equals(CDS))
                      r = Range.closed(codingLength,codingLength+(end-cdsStart));
@@ -973,6 +981,7 @@ private static List<Range> getCDSExonRangesReverse(GeneChromosomePosition chromP
 
             } else if (inCoding) {
                 // full exon is coding
+
                 Range r;
                 if ( responseType.equals(CDS))
                      r = Range.closed(codingLength,codingLength+(end-start));
@@ -1003,6 +1012,7 @@ private static List<Range> getCDSExonRangesReverse(GeneChromosomePosition chromP
     }
 
 
+
     private static List<Range> getCDSExonRangesForward(GeneChromosomePosition chromPos,
                                                        String responseType) {
 
@@ -1028,6 +1038,7 @@ private static List<Range> getCDSExonRangesForward(GeneChromosomePosition chromP
                 codingLength += (end - cdsStart);
 //
 
+
                 Range r;
                 if ( responseType.equals(CDS))
                     r = Range.closed(0,codingLength);
@@ -1039,6 +1050,7 @@ private static List<Range> getCDSExonRangesForward(GeneChromosomePosition chromP
                 //System.out.println(" <-- CDS end at: " + cdsEnd );
                 inCoding = false;
 
+
                 Range r;
                 if ( responseType.equals(CDS))
                      r = Range.closed(codingLength,codingLength+(cdsEnd-start));
@@ -1049,6 +1061,7 @@ private static List<Range> getCDSExonRangesForward(GeneChromosomePosition chromP
 
             } else if (inCoding) {
                 // full exon is coding
+
                 Range r;
                 if ( responseType.equals(CDS))
                     r = Range.closed(codingLength,codingLength+(end-start));
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java
@@ -79,7 +79,7 @@ public void testAK1() {
                 chromranges = Lists.reverse(chromranges);
 
                 assertTrue(chromranges.size() == 6);
-                
+
                 // compare with https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=CCDS6881
                 validateExon(0,127868008,127868076, chromranges  );
                 validateExon(1,127868320,127868512, chromranges  );
