biojava#534 renaming method names, according to @joseduarte 's comments

andreasprlic · andreasprlic · commit aba6ed8f22ae · 2016-07-27T13:26:05.000-07:00
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
@@ -46,11 +46,11 @@ public static String formatExonStructure(GeneChromosomePosition chromosomePositi
      * @param chromosomePosition
      * @return
      */
-    public static String printHTMLExonStructure(GeneChromosomePosition chromosomePosition ){
+    public static String getHTMLExonStructure(GeneChromosomePosition chromosomePosition ){
         if ( chromosomePosition.getOrientation() == '+')
-            return printHTMLExonStructureForward(chromosomePosition);
+            return getHTMLExonStructureForward(chromosomePosition);
 
-        return printHTMLExonStructureReverse(chromosomePosition);
+        return getHTMLExonStructureReverse(chromosomePosition);
 
     }
 
@@ -108,7 +108,7 @@ private static String formatExonStructureForward(GeneChromosomePosition chromPos
     }
 
 
-    private static String printHTMLExonStructureForward(GeneChromosomePosition chromPos) {
+    private static String getHTMLExonStructureForward(GeneChromosomePosition chromPos) {
         StringWriter s = new StringWriter();
 
         List<Integer> exonStarts = chromPos.getExonStarts();
@@ -189,7 +189,7 @@ private static String showGenePosLink(GeneChromosomePosition chromPos, Integer p
         return buf.toString();
     }
 
-    private static String printHTMLExonStructureReverse(GeneChromosomePosition chromPos) {
+    private static String getHTMLExonStructureReverse(GeneChromosomePosition chromPos) {
         StringWriter s = new StringWriter();
 
         List<Integer> exonStarts = chromPos.getExonStarts();
@@ -783,7 +783,7 @@ public static int getCDSLengthReverse(List<Integer> exonStarts,
 
                 logger.debug(" no translation!");
             }
-            
+
         }
 
         logger.debug("length exons: " + lengthExons + " codin length: " + (codingLength - 3));

Original file line number	Diff line number	Diff line change
`@@ -46,11 +46,11 @@ public static String formatExonStructure(GeneChromosomePosition chromosomePositi`
`46`	`46`	`* @param chromosomePosition`
`47`	`47`	`* @return`
`48`	`48`	`*/`
`49`		`- public static String printHTMLExonStructure(GeneChromosomePosition chromosomePosition ){`
	`49`	`+ public static String getHTMLExonStructure(GeneChromosomePosition chromosomePosition ){`
`50`	`50`	`if ( chromosomePosition.getOrientation() == '+')`
`51`		`- return printHTMLExonStructureForward(chromosomePosition);`
	`51`	`+ return getHTMLExonStructureForward(chromosomePosition);`
`52`	`52`
`53`		`- return printHTMLExonStructureReverse(chromosomePosition);`
	`53`	`+ return getHTMLExonStructureReverse(chromosomePosition);`
`54`	`54`
`55`	`55`	`}`
`56`	`56`
`@@ -108,7 +108,7 @@ private static String formatExonStructureForward(GeneChromosomePosition chromPos`
`108`	`108`	`}`
`109`	`109`
`110`	`110`
`111`		`- private static String printHTMLExonStructureForward(GeneChromosomePosition chromPos) {`
	`111`	`+ private static String getHTMLExonStructureForward(GeneChromosomePosition chromPos) {`
`112`	`112`	`StringWriter s = new StringWriter();`
`113`	`113`
`114`	`114`	`List<Integer> exonStarts = chromPos.getExonStarts();`
`@@ -189,7 +189,7 @@ private static String showGenePosLink(GeneChromosomePosition chromPos, Integer p`
`189`	`189`	`return buf.toString();`
`190`	`190`	`}`
`191`	`191`
`192`		`- private static String printHTMLExonStructureReverse(GeneChromosomePosition chromPos) {`
	`192`	`+ private static String getHTMLExonStructureReverse(GeneChromosomePosition chromPos) {`
`193`	`193`	`StringWriter s = new StringWriter();`
`194`	`194`
`195`	`195`	`List<Integer> exonStarts = chromPos.getExonStarts();`
`@@ -783,7 +783,7 @@ public static int getCDSLengthReverse(List<Integer> exonStarts,`
`783`	`783`
`784`	`784`	`logger.debug(" no translation!");`
`785`	`785`	`}`
`786`		`-`
	`786`	`+`
`787`	`787`	`}`
`788`	`788`
`789`	`789`	`logger.debug("length exons: " + lengthExons + " codin length: " + (codingLength - 3));`