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andreasprlicandreasprlic
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biojava#534 moving the getHTML methods out of BioJava
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‎biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java‎

Lines changed: 1 addition & 159 deletions
Original file line numberDiff line numberDiff line change
@@ -39,20 +39,7 @@ public static String formatExonStructure(GeneChromosomePosition chromosomePositi
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return formatExonStructureReverse(chromosomePosition);
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}
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/** Pretty print the details of a GeneChromosomePosition in a HTML-formatted string
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*
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* @param chromosomePosition
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* @return
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*/
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public static String getHTMLExonStructure(GeneChromosomePosition chromosomePosition ){
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if ( chromosomePosition.getOrientation() == '+')
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return getHTMLExonStructureForward(chromosomePosition);
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return getHTMLExonStructureReverse(chromosomePosition);
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}
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private static String formatExonStructureForward(GeneChromosomePosition chromPos) {
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@@ -108,68 +95,6 @@ private static String formatExonStructureForward(GeneChromosomePosition chromPos
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}
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private static String getHTMLExonStructureForward(GeneChromosomePosition chromPos) {
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StringWriter s = new StringWriter();
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List<Integer> exonStarts = chromPos.getExonStarts();
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List<Integer> exonEnds = chromPos.getExonEnds();
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int cdsStart = chromPos.getCdsStart();
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int cdsEnd = chromPos.getCdsEnd();
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boolean inCoding = false;
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int codingLength = 0;
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for (int i = 0; i < exonStarts.size(); i++) {
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int start = exonStarts.get(i);
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int end = exonEnds.get(i);
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//s.append("forward exon: " + start + " - " + end + " | " + (end - start));
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//s.append(newline);
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if (start <= cdsStart && end >= cdsStart) {
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inCoding = true;
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codingLength += (end - cdsStart);
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s.append("<tr><th>Region</th><th>start</th><th>end</th><th>region length</th><th>phase at end</th></tr>");
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s.append("<tr><td>UTR</td><td>" + format(start) + "</td><td>" + format(cdsStart) + "</td><td></td><td></td></tr>");
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s.append(newline);
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s.append("<tr><td>Exon</td><td>").append(showGenePosLink(chromPos, (cdsStart + 1))).append("</td><td>").append(showGenePosLink(chromPos, end)).append("</td><td>").append(Integer.toString(end - cdsStart)).append("</td><td>").append(Integer.toString(codingLength % 3)).append("</td></tr>");
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s.append(newline);
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} else if (start <= cdsEnd && end >= cdsEnd) {
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//logger.debug(" <-- CDS end at: " + cdsEnd );
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inCoding = false;
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codingLength += (cdsEnd - start);
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s.append("<tr><td>Exon</td><td>" + showGenePosLink(chromPos, (start + 1)) + "</td><td>" + showGenePosLink(chromPos,cdsEnd) + "</td><td>" + (cdsEnd - start) + "</td><td>" + (codingLength % 3)+"</td></tr>");
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s.append(newline);
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s.append("<tr><td>UTR</td><td>" + format(cdsEnd +1) + "</td><td>" + format(end)+"</td><td></td><td></td></tr>");
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s.append(newline);
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} else if (inCoding) {
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// full exon is coding
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codingLength += (end - start);
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s.append("<tr><td>Exon</td><td>").append(showGenePosLink(chromPos, (start + 1))).append("</td><td>").append(showGenePosLink(chromPos, end)).append("</td><td>").append(Integer.toString(end - start)).append("</td><td>").append(Integer.toString(codingLength % 3)).append("</td></tr>");
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s.append(newline);
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}
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// if ( inCoding )
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// logger.debug("exon phase at end:" + (codingLength % 3));
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//
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// logger.debug(" coding length: " + codingLength);
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}
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//s.append("Length of coding sequence: ");
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//s.append((codingLength-3)+" nucleotides.");
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s.append(newline);
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return s.toString();
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}
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private static String showGenePosLink(GeneChromosomePosition chromPos, Integer pos ) {
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@@ -189,89 +114,6 @@ private static String showGenePosLink(GeneChromosomePosition chromPos, Integer p
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return buf.toString();
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}
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private static String getHTMLExonStructureReverse(GeneChromosomePosition chromPos) {
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StringWriter s = new StringWriter();
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List<Integer> exonStarts = chromPos.getExonStarts();
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List<Integer> exonEnds = chromPos.getExonEnds();
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int cdsStart = chromPos.getCdsStart();
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int cdsEnd = chromPos.getCdsEnd();
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// logger.debug("CDS START:" +format(cdsStart) + " - " + format(cdsEnd));
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boolean inCoding = false;
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int codingLength = 0;
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if (cdsEnd < cdsStart) {
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int tmp = cdsEnd;
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cdsEnd = cdsStart;
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cdsStart = tmp;
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}
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s.append("<tr><th>Region</th><th>start</th><th>end</th><th>region length</th><th>phase at end</th></tr>");
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// map reverse
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for (int i = exonStarts.size() - 1; i >= 0; i--) {
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int end = exonStarts.get(i);
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int start = exonEnds.get(i);
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if (end < start) {
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int tmp = end;
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end = start;
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start = tmp;
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}
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if (start <= cdsEnd && end >= cdsEnd) {
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inCoding = true;
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int tmpstart = start;
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if (start < cdsStart) {
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tmpstart = cdsStart;
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}
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codingLength += (cdsEnd - tmpstart);
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s.append("<tr><td><div data-toggle=\"tooltip\" data-placement=\"top\" title=\"Untranslated Region\">UTR</div></td><td>").append(format(cdsEnd + 1)).append("</td><td>").append(format(end)).append("</td><td></td><td></td></tr>");
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s.append(newline);
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s.append("<tr><td>Exon</td><td>" + showGenePosLink(chromPos,(tmpstart+1)) + "</td><td>" + showGenePosLink(chromPos, cdsEnd) + "</td><td>" + (cdsEnd - tmpstart) + "</td><td>" + (codingLength % 3)+"</td></tr>");
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s.append(newline);
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// single exon with UTR on both ends
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if (tmpstart != start)
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s.append("<tr><td><div data-toggle=\"tooltip\" data-placement=\"top\" title=\"Untranslated Region\">UTR</div></td><td>" + format(cdsStart) + "</td><td>" + format(start + 1) + "</td><td></td><td></td></tr>");
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s.append(newline);
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} else if (start <= cdsStart && end >= cdsStart) {
247-
inCoding = false;
248-
codingLength += (end - cdsStart);
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s.append("<tr><td>Exon</td><td>" + showGenePosLink(chromPos,(cdsStart+1)) + "</td><td>" + showGenePosLink(chromPos, end) + "</td><td>" + (end - cdsStart) +"</td><td>"+ (codingLength % 3)+"</td></tr>");
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s.append(newline);
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s.append("<tr><td><div data-toggle=\"tooltip\" data-placement=\"top\" title=\"Untranslated Region\">UTR</div></td><td>" + format(start+1) + "</td><td>" + format(cdsStart)+"</td><td></td><td></td></tr>");
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s.append(newline);
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} else if (inCoding) {
257-
// full exon is coding
258-
codingLength += (end - start);
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260-
s.append("<tr><td>Exon</td><td>" + showGenePosLink(chromPos,(start+1)) + "</td><td>" + showGenePosLink(chromPos, end) + "</td><td>" + (end - start) + "</td><td>" + (codingLength % 3)+"</td></tr>");
261-
s.append(newline);
262-
} else {
263-
// e.g. see UBQLN3
264-
s.append("<tr><td data-toggle=\"tooltip\" data-placement=\"right\" title=\"Untranslated Region\">UTR</td><td>" + format(start) + "</td><td>" + format(end)+"</td><td></td><td></td></tr>");
265-
s.append(newline);
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}
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}
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// s.append("Length coding sequence: " + (codingLength-3) + " nucleotides");
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s.append(newline);
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return s.toString();
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}
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276118
private static String formatExonStructureReverse(GeneChromosomePosition chromPos) {
277119
StringWriter s = new StringWriter();

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