firstRNA1stBaseSecondRNA1stBaseFirstRNA2ndBaseSecondRNA2ndBase [...]
+ * AAC-GUAGA--UGG
+ * @param struct
+ * - The super-structure
+ * @param basesOwn
+ * - The RNA owning bases array (each index will be:0 when common
+ * base, 1 when first RNA alignment base, 2 when second RNA
+ * alignment base)
+ * @throws ExceptionUnmatchedClosingParentheses
+ * @throws ExceptionFileFormatOrSyntax
+ */
+ public void setRNA(String seq, String struct, ArrayListnum, -1 of no such base model exists.
+ */
+
+ public int getIndexFromBaseNumber(int num) {
+ for (int i = 0; i < this._listeBases.size(); i++) {
+ if (_listeBases.get(i).getBaseNumber() == num) {
+ return i;
+ }
+ }
+ return -1;
+ }
+
+ /**
+ * Adds a base pair to this RNA's structure. Tries to add it to the
+ * secondary structure first, eventually adding it to the 'tertiary'
+ * interactions if it clashes with the current secondary structure.
+ *
+ * @param baseNumber5
+ * - Base number of the origin of this base pair
+ * @param baseNumber3
+ * - Base number of the destination of this base pair
+ */
+
+ public void addBPToStructureUsingNumbers(int baseNumber5, int baseNumber3) {
+ int i = getIndexFromBaseNumber(baseNumber5);
+ int j = getIndexFromBaseNumber(baseNumber3);
+ addBP(i, j);
+ }
+
+ /**
+ * Adds a base pair to this RNA's structure. Tries to add it to the
+ * secondary structure first, possibly adding it to the 'tertiary'
+ * interactions if it clashes with the current secondary structure.
+ *
+ * @param number5
+ * - Base number of the origin of this base pair
+ * @param number3
+ * - Base number of the destination of this base pair
+ */
+
+ public void addBPToStructureUsingNumbers(int number5, int number3,
+ ModeleBP msbp) {
+ addBP(getIndexFromBaseNumber(number5), getIndexFromBaseNumber(number3),
+ msbp);
+ }
+
+ public void addBP(int index5, int index3) {
+ int i = index5;
+ int j = index3;
+ ModeleBase part5 = _listeBases.get(i);
+ ModeleBase part3 = _listeBases.get(j);
+ ModeleBP msbp = new ModeleBP(part5, part3);
+ addBP(i, j, msbp);
+ }
+
+ public void addBP(int index5, int index3, ModeleBP msbp) {
+ int i = index5;
+ int j = index3;
+
+ if (j < i) {
+ int k = j;
+ j = i;
+ i = k;
+ }
+ if (i != -1) {
+ for (int k = i; k <= j; k++) {
+ ModeleBase tmp = _listeBases.get(k);
+ int l = tmp.getElementStructure();
+ if (l != -1) {
+ if ((l <= i) || (l >= j)) {
+ addBPAux(i, j, msbp);
+ return;
+ }
+ }
+ }
+ addBPnow(i, j, msbp);
+ }
+ }
+
+ public void removeBP(ModeleBP ms) {
+ if (_structureAux.contains(ms)) {
+ _structureAux.remove(ms);
+ } else {
+ ModeleBase m5 = ms.getPartner5();
+ ModeleBase m3 = ms.getPartner3();
+ int i = m5.getIndex();
+ int j = m3.getIndex();
+ if ((m5.getElementStructure() == m3.getIndex())
+ && (m3.getElementStructure() == m5.getIndex())) {
+ m5.removeElementStructure();
+ m3.removeElementStructure();
+ }
+ }
+ }
+
+ /**
+ * Register base-pair, no question asked. More precisely, this function will
+ * not try to determine if the base-pairs crosses any other.
+ *
+ * @param i
+ * @param j
+ * @param msbp
+ */
+ private void addBPNow(int i, int j) {
+ if (j < i) {
+ int k = j;
+ j = i;
+ i = k;
+ }
+
+ ModeleBase part5 = _listeBases.get(i);
+ ModeleBase part3 = _listeBases.get(j);
+ ModeleBP msbp = new ModeleBP(part5, part3);
+ addBPnow(i, j, msbp);
+ }
+
+ /**
+ * Register base-pair, no question asked. More precisely, this function will
+ * not try to determine if the base-pairs crosses any other.
+ *
+ * @param i
+ * @param j
+ * @param msbp
+ */
+ private void addBPnow(int i, int j, ModeleBP msbp) {
+ if (j < i) {
+ int k = j;
+ j = i;
+ i = k;
+ }
+ ModeleBase part5 = _listeBases.get(i);
+ ModeleBase part3 = _listeBases.get(j);
+ msbp.setPartner5(part5);
+ msbp.setPartner3(part3);
+ part5.setElementStructure(j, msbp);
+ part3.setElementStructure(i, msbp);
+ }
+
+ public void addBPAux(int i, int j) {
+ ModeleBase part5 = _listeBases.get(i);
+ ModeleBase part3 = _listeBases.get(j);
+ ModeleBP msbp = new ModeleBP(part5, part3);
+ addBPAux(i, j, msbp);
+ }
+
+ public void addBPAux(int i, int j, ModeleBP msbp) {
+ if (j < i) {
+ int k = j;
+ j = i;
+ i = k;
+ }
+ ModeleBase part5 = _listeBases.get(i);
+ ModeleBase part3 = _listeBases.get(j);
+ msbp.setPartner5(part5);
+ msbp.setPartner3(part3);
+ _structureAux.add(msbp);
+ }
+
+ public ArrayListindex. Indices are contiguous in
+ * the sequence over an interval [0,this.getSize()-1], where
+ * n is the length of the sequence.
+ *
+ * @param index
+ * The index, 0 ≤ index < this.getSize(), of the
+ * base model
+ * @return The base model of index index
+ */
+ public ModeleBase getBaseAt(int index) {
+ return this._listeBases.get(index);
+ }
+
+ /**
+ * Returns the set of bases of indices in indices. Indices are
+ * contiguous in the sequence, and belong to an interval
+ * [0,n-1], where n is the length of the sequence.
+ *
+ * @param indices
+ * A Collection of indices i,
+ * 0 ≤ index < this.getSize(), where some base
+ * models are found.
+ * @return A list of base model of indices in indices
+ */
+ public ArrayList| Name: | " + this._name + " |
| Length: | " + this.getSize() + + " nts |
| Base-pairs: | " + + this.getAllBPs().size() + " |