+++ /dev/null
-/*
- VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases.
- Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty.
- electronic mail : Yann.Ponty@lri.fr
- paper mail : LRI, bat 490 Université Paris-Sud 91405 Orsay Cedex France
-
- This file is part of VARNA version 3.1.
- VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License
- as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
-
- VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
- without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
- See the GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License along with VARNA version 3.1.
- If not, see http://www.gnu.org/licenses.
- */
-package fr.orsay.lri.varna.models.naView;
-
-
-import java.util.ArrayList;
-
-import fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm;
-import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
-import fr.orsay.lri.varna.interfaces.InterfaceVARNAObservable;
-
-public class NAView {
- private final double ANUM = 9999.0;
- private final int MAXITER = 500;
-
- private ArrayList<Base> bases;
- private int nbase, nregion, loop_count;
-
- private Loop root = new Loop();
- private ArrayList<Loop> loops;
-
- private ArrayList<Region> regions;
-
- private Radloop rlphead = new Radloop();
-
- private double lencut=0.8;
- private final double RADIUS_REDUCTION_FACTOR = 1.4;
-
- // show algorithm step by step
- private boolean debug = false;
-
- private double angleinc;
-
- private double _h;
-
- private ArrayList<InterfaceVARNAListener> _listeVARNAListener = new ArrayList<InterfaceVARNAListener>();
-
- private boolean noIterationFailureYet = true;
-
- double HELIX_FACTOR = 0.6;
- double BACKBONE_DISTANCE = 27;
-
- public int naview_xy_coordinates(ArrayList<Short> pair_table2,
- ArrayList<Double> x, ArrayList<Double> y)
- throws ExceptionNAViewAlgorithm {
- if (debug)
- System.out.println("naview_xy_coordinates");
- if (pair_table2.size() == 0)
- return 0;
- int i;
- ArrayList<Integer> pair_table = new ArrayList<Integer>(pair_table2
- .size() + 1);
- pair_table.add(pair_table2.size());
-
- for (int j = 0; j < pair_table2.size(); j++) {
- pair_table.add(pair_table2.get(j) + 1);
- }
-
- if (debug) {
- infoStructure(pair_table);
- }
- // length
- nbase = pair_table.get(0);
- bases = new ArrayList<Base>(nbase + 1);
-
- for (int index = 0; index < bases.size(); index++) {
- bases.add(new Base());
- }
-
- regions = new ArrayList<Region>();
- for (int index = 0; index < nbase + 1; index++) {
- regions.add(new Region());
- }
-
- read_in_bases(pair_table);
-
- if (debug)
- infoBasesMate();
-
- rlphead = null;
-
- find_regions();
-
- if (debug)
- infoRegions();
-
- loop_count = 0;
- loops = new ArrayList<Loop>(nbase + 1);
- for (int index = 0; index < nbase + 1; index++) {
- loops.add(new Loop());
- }
-
- construct_loop(0);
-
- if (debug)
- infoBasesExtracted();
-
- find_central_loop();
-
- if (debug)
- infoRoot();
-
- if (debug)
- dump_loops();
-
- traverse_loop(root, null);
-
- for (i = 0; i < nbase; i++) {
- x.add(100 + BACKBONE_DISTANCE * bases.get(i + 1).getX());
- y.add(100 + BACKBONE_DISTANCE * bases.get(i + 1).getY());
- }
-
- return nbase;
- }
-
- private void infoStructure(ArrayList<Integer> pair_table) {
- System.out.println("structure:");
- for (int j = 0; j < pair_table.size(); j++) {
- System.out.print("#" + j + ":" + pair_table.get(j) + "\t");
- if (j % 10 == 0)
- System.out.println();
- }
- System.out.println();
- }
-
- private void infoBasesMate() {
- System.out.println("Bases mate:");
- for (int index = 0; index < bases.size(); index++) {
- System.out.print("#" + index + ":" + bases.get(index).getMate()
- + "\t");
- if (index % 10 == 0)
- System.out.println();
- }
- System.out.println();
- }
-
- private void infoRegions() {
- System.out.println("regions:");
- for (int index = 0; index < regions.size(); index++) {
- System.out.print("(" + regions.get(index).getStart1() + ","
- + regions.get(index).getStart2() + ";"
- + regions.get(index).getEnd1() + ","
- + regions.get(index).getEnd2() + ")\t\t");
- if (index % 5 == 0)
- System.out.println();
- }
- System.out.println();
- }
-
- private void infoBasesExtracted() {
- System.out.println("Bases extracted:");
- for (int index = 0; index < bases.size(); index++) {
- System.out.print("i=" + index + ":"
- + bases.get(index).isExtracted() + "\t");
- if (index % 5 == 0)
- System.out.println();
- }
- System.out.println();
- }
-
- private void infoRoot() {
- System.out.println("root" + root.getNconnection() + ";"
- + root.getNumber());
- System.out.println("\troot : ");
- System.out.println("\tdepth=" + root.getDepth());
- System.out.println("\tmark=" + root.isMark());
- System.out.println("\tnumber=" + root.getNumber());
- System.out.println("\tradius=" + root.getRadius());
- System.out.println("\tx=" + root.getX());
- System.out.println("\ty=" + root.getY());
- System.out.println("\tnconnection=" + root.getNconnection());
- }
-
- private void read_in_bases(ArrayList<Integer> pair_table) {
- if (debug)
- System.out.println("read_in_bases");
-
- int i, npairs;
-
- // Set up an origin.
- bases.add(new Base());
- bases.get(0).setMate(0);
- bases.get(0).setExtracted(false);
- bases.get(0).setX(ANUM);
- bases.get(0).setY(ANUM);
-
- for (npairs = 0, i = 1; i <= nbase; i++) {
- bases.add(new Base());
- bases.get(i).setExtracted(false);
- bases.get(i).setX(ANUM);
- bases.get(i).setY(ANUM);
- bases.get(i).setMate(pair_table.get(i));
- if ((int) pair_table.get(i) > i)
- npairs++;
- }
- // must have at least 1 pair to avoid segfault
- if (npairs == 0) {
- bases.get(1).setMate(nbase);
- bases.get(nbase).setMate(1);
- }
- }
-
- /**
- * Identifies the regions in the structure.
- */
- private void find_regions()
-
- {
- if (debug)
- System.out.println("find_regions");
- int i, mate, nb1;
- nb1 = nbase + 1;
- ArrayList<Boolean> mark = new ArrayList<Boolean>(nb1);
- for (i = 0; i < nb1; i++)
- mark.add(false);
- nregion = 0;
- for (i = 0; i <= nbase; i++) {
- if ((mate = bases.get(i).getMate()) != 0 && !mark.get(i)) {
- regions.get(nregion).setStart1(i);
- regions.get(nregion).setEnd2(mate);
- mark.set(i, true);
- mark.set(mate, true);
- bases.get(i).setRegion(regions.get(nregion));
- bases.get(mate).setRegion(regions.get(nregion));
- for (i++, mate--; i < mate && bases.get(i).getMate() == mate; i++, mate--) {
- mark.set(mate, true);
- mark.set(i, true);
- bases.get(i).setRegion(regions.get(nregion));
- bases.get(mate).setRegion(regions.get(nregion));
- }
- regions.get(nregion).setEnd1(--i);
- regions.get(nregion).setStart2(mate + 1);
- if (debug) {
- if (nregion == 0)
- System.out.printf("\nRegions are:\n");
- System.out.printf(
- "Region %d is %d-%d and %d-%d with gap of %d.\n",
- nregion + 1, regions.get(nregion).getStart1(),
- regions.get(nregion).getEnd1(), regions
- .get(nregion).getStart2(), regions.get(
- nregion).getEnd2(), regions.get(nregion)
- .getStart2()
- - regions.get(nregion).getEnd1() + 1);
- }
- nregion++;
- }
- }
- }
-
- /**
- * Starting at residue ibase, recursively constructs the loop containing
- * said base and all deeper bases.
- *
- * @throws ExceptionNAViewAlgorithm
- */
- private Loop construct_loop(int ibase) throws ExceptionNAViewAlgorithm {
- if (debug)
- System.out.println("construct_loop");
- int i, mate;
- Loop retloop = new Loop(), lp = new Loop();
- Connection cp = new Connection();
- Region rp = new Region();
- Radloop rlp = new Radloop();
- retloop = loops.get(loop_count++);
- retloop.setNconnection(0);
- //System.out.println(""+ibase+" "+nbase);
- //ArrayList<Connection> a = new ArrayList<Connection>(nbase + 1);
- //retloop.setConnections(a);
-// for (int index = 0; index < nbase + 1; index++)
-// retloop.getConnections().add(new Connection());
- //for (int index = 0; index < nbase + 1; index++)
- // retloop.addConnection(index,new Connection());
- retloop.setDepth(0);
- retloop.setNumber(loop_count);
- retloop.setRadius(0.0);
- for (rlp = rlphead; rlp != null; rlp = rlp.getNext())
- if (rlp.getLoopnumber() == loop_count)
- retloop.setRadius(rlp.getRadius());
- i = ibase;
- do {
- if ((mate = bases.get(i).getMate()) != 0) {
- rp = bases.get(i).getRegion();
- if (!bases.get(rp.getStart1()).isExtracted()) {
- if (i == rp.getStart1()) {
- bases.get(rp.getStart1()).setExtracted(true);
- bases.get(rp.getEnd1()).setExtracted(true);
- bases.get(rp.getStart2()).setExtracted(true);
- bases.get(rp.getEnd2()).setExtracted(true);
- lp = construct_loop(rp.getEnd1() < nbase ? rp.getEnd1() + 1
- : 0);
- } else if (i == rp.getStart2()) {
- bases.get(rp.getStart2()).setExtracted(true);
- bases.get(rp.getEnd2()).setExtracted(true);
- bases.get(rp.getStart1()).setExtracted(true);
- bases.get(rp.getEnd1()).setExtracted(true);
- lp = construct_loop(rp.getEnd2() < nbase ? rp.getEnd2() + 1
- : 0);
- } else {
- throw new ExceptionNAViewAlgorithm(
- "naview:Error detected in construct_loop. i = "
- + i + " not found in region table.\n");
- }
- retloop.setNconnection(retloop.getNconnection() + 1);
- cp = new Connection();
- retloop.setConnection(retloop.getNconnection() - 1, cp);
- retloop.setConnection(retloop.getNconnection(), null);
- cp.setLoop(lp);
- cp.setRegion(rp);
- if (i == rp.getStart1()) {
- cp.setStart(rp.getStart1());
- cp.setEnd(rp.getEnd2());
- } else {
- cp.setStart(rp.getStart2());
- cp.setEnd(rp.getEnd1());
- }
- cp.setExtruded(false);
- cp.setBroken(false);
- lp.setNconnection(lp.getNconnection() + 1);
- cp = new Connection();
- lp.setConnection(lp.getNconnection() - 1, cp);
- lp.setConnection(lp.getNconnection(), null);
- cp.setLoop(retloop);
- cp.setRegion(rp);
- if (i == rp.getStart1()) {
- cp.setStart(rp.getStart2());
- cp.setEnd(rp.getEnd1());
- } else {
- cp.setStart(rp.getStart1());
- cp.setEnd(rp.getEnd2());
- }
- cp.setExtruded(false);
- cp.setBroken(false);
- }
- i = mate;
- }
- if (++i > nbase)
- i = 0;
- } while (i != ibase);
- return retloop;
- }
-
- /**
- * Displays all the loops.
- */
- private void dump_loops() {
- System.out.println("dump_loops");
- int il, ilp, irp;
- Loop lp;
- Connection cp;
-
- System.out.printf("\nRoot loop is #%d\n", loops.indexOf(root) + 1);
- for (il = 0; il < loop_count; il++) {
- lp = loops.get(il);
- System.out.printf("Loop %d has %d connections:\n", il + 1, lp
- .getNconnection());
- for (int i = 0; (cp = lp.getConnection(i)) != null; i++) {
- ilp = (loops.indexOf(cp.getLoop())) + 1;
- irp = (regions.indexOf(cp.getRegion())) + 1;
- System.out.printf(" Loop %d Region %d (%d-%d)\n", ilp, irp, cp
- .getStart(), cp.getEnd());
- }
- }
- }
-
- /**
- * Find node of greatest branching that is deepest.
- */
- private void find_central_loop() {
- if (debug)
- System.out.println("find_central_loop");
- Loop lp = new Loop();
- int maxconn, maxdepth, i;
-
- determine_depths();
- maxconn = 0;
- maxdepth = -1;
- for (i = 0; i < loop_count; i++) {
- lp = loops.get(i);
- if (lp.getNconnection() > maxconn) {
- maxdepth = lp.getDepth();
- maxconn = lp.getNconnection();
- root = lp;
- } else if (lp.getDepth() > maxdepth
- && lp.getNconnection() == maxconn) {
- maxdepth = lp.getDepth();
- root = lp;
- }
- }
- }
-
- /**
- * Determine the depth of all loops.
- */
- private void determine_depths() {
- if (debug)
- System.out.println("determine_depths");
- Loop lp = new Loop();
- int i, j;
-
- for (i = 0; i < loop_count; i++) {
- lp = loops.get(i);
- for (j = 0; j < loop_count; j++)
- loops.get(j).setMark(false);
- lp.setDepth(depth(lp));
- }
- }
-
- /**
- * Determines the depth of loop, lp. Depth is defined as the minimum
- * distance to a leaf loop where a leaf loop is one that has only one or no
- * connections.
- */
- private int depth(Loop lp) {
- if (debug)
- System.out.println("depth");
- int count, ret, d;
-
- if (lp.getNconnection() <= 1)
- return 0;
- if (lp.isMark())
- return -1;
- lp.setMark(true);
- count = 0;
- ret = 0;
- for (int i = 0; lp.getConnection(i) != null; i++) {
- d = depth(lp.getConnection(i).getLoop());
- if (d >= 0) {
- if (++count == 1)
- ret = d;
- else if (ret > d)
- ret = d;
- }
- }
- lp.setMark(false);
- return ret + 1;
- }
-
- /**
- * This is the workhorse of the display program. The algorithm is recursive
- * based on processing individual loops. Each base pairing region is
- * displayed using the direction given by the circle diagram, and the
- * connections between the regions is drawn by equally spaced points. The
- * radius of the loop is set to minimize the square error for lengths
- * between sequential bases in the loops. The "correct" length for base
- * links is 1. If the least squares fitting of the radius results in loops
- * being less than 1/2 unit apart, then that segment is extruded.
- *
- * The variable, anchor_connection, gives the connection to the loop
- * processed in an previous level of recursion.
- *
- * @throws ExceptionNAViewAlgorithm
- */
- private void traverse_loop(Loop lp, Connection anchor_connection)
- throws ExceptionNAViewAlgorithm {
- if (debug)
- System.out.println(" traverse_loop");
- double xs, ys, xe, ye, xn, yn, angleinc, r;
- double radius, xc, yc, xo, yo, astart, aend, a;
- Connection cp, cpnext, acp, cpprev;
- int i, j, n, ic;
- double da, maxang;
- int count, icstart, icend, icmiddle, icroot;
- boolean done, done_all_connections, rooted;
- int sign;
- double midx, midy, nrx, nry, mx, my, vx, vy, dotmv, nmidx, nmidy;
- int icstart1, icup, icdown, icnext, direction;
- double dan, dx, dy, rr;
- double cpx, cpy, cpnextx, cpnexty, cnx, cny, rcn, rc, lnx, lny, rl, ac, acn, sx, sy, dcp;
- int imaxloop = 0;
-
- angleinc = 2 * Math.PI / (nbase + 1);
- acp = null;
- icroot = -1;
- int indice = 0;
-
- for (ic = 0; (cp = lp.getConnection(indice)) != null; indice++, ic++) {
- // xs = cos(angleinc*cp.setStart(); ys = sin(angleinc*cp.setStart();
- // xe =
- // cos(angleinc*cp.setEnd()); ye = sin(angleinc*cp.setEnd());
- xs = -Math.sin(angleinc * cp.getStart());
- ys = Math.cos(angleinc * cp.getStart());
- xe = -Math.sin(angleinc * cp.getEnd());
- ye = Math.cos(angleinc * cp.getEnd());
- xn = ye - ys;
- yn = xs - xe;
- r = Math.sqrt(xn * xn + yn * yn);
- cp.setXrad(xn / r);
- cp.setYrad(yn / r);
- cp.setAngle(Math.atan2(yn, xn));
- if (cp.getAngle() < 0.0)
- cp.setAngle(cp.getAngle() + 2 * Math.PI);
- if (anchor_connection != null
- && anchor_connection.getRegion() == cp.getRegion()) {
- acp = cp;
- icroot = ic;
- }
- }
- // remplacement d'une etiquette de goto
- set_radius: while (true) {
- determine_radius(lp, lencut);
- radius = lp.getRadius()/RADIUS_REDUCTION_FACTOR;
- if (anchor_connection == null)
- xc = yc = 0.0;
- else {
- xo = (bases.get(acp.getStart()).getX() + bases
- .get(acp.getEnd()).getX()) / 2.0;
- yo = (bases.get(acp.getStart()).getY() + bases
- .get(acp.getEnd()).getY()) / 2.0;
- xc = xo - radius * acp.getXrad();
- yc = yo - radius * acp.getYrad();
- }
-
- // The construction of the connectors will proceed in blocks of
- // connected connectors, where a connected connector pairs means two
- // connectors that are forced out of the drawn circle because they
- // are too close together in angle.
-
- // First, find the start of a block of connected connectors
-
- if (icroot == -1)
- icstart = 0;
- else
- icstart = icroot;
- cp = lp.getConnection(icstart);
- count = 0;
- if (debug)
- {
- System.out.printf("Now processing loop %d\n", lp.getNumber());
- System.out.println(" "+lp);
- }
- done = false;
- do {
- j = icstart - 1;
- if (j < 0)
- j = lp.getNconnection() - 1;
- cpprev = lp.getConnection(j);
- if (!connected_connection(cpprev, cp)) {
- done = true;
- } else {
- icstart = j;
- cp = cpprev;
- }
- if (++count > lp.getNconnection()) {
- // Here everything is connected. Break on maximum angular
- // separation between connections.
-
- maxang = -1.0;
- for (ic = 0; ic < lp.getNconnection(); ic++) {
- j = ic + 1;
- if (j >= lp.getNconnection())
- j = 0;
- cp = lp.getConnection(ic);
- cpnext = lp.getConnection(j);
- ac = cpnext.getAngle() - cp.getAngle();
- if (ac < 0.0)
- ac += 2 * Math.PI;
- if (ac > maxang) {
- maxang = ac;
- imaxloop = ic;
- }
- }
- icend = imaxloop;
- icstart = imaxloop + 1;
- if (icstart >= lp.getNconnection())
- icstart = 0;
- cp = lp.getConnection(icend);
- cp.setBroken(true);
- done = true;
- }
- } while (!done);
- done_all_connections = false;
- icstart1 = icstart;
- if (debug)
- System.out.printf(" Icstart1 = %d\n", icstart1);
- while (!done_all_connections) {
- count = 0;
- done = false;
- icend = icstart;
- rooted = false;
- while (!done) {
- cp = lp.getConnection(icend);
- if (icend == icroot)
- rooted = true;
- j = icend + 1;
- if (j >= lp.getNconnection()) {
- j = 0;
- }
- cpnext = lp.getConnection(j);
- if (connected_connection(cp, cpnext)) {
- if (++count >= lp.getNconnection())
- break;
- icend = j;
- } else {
- done = true;
- }
- }
- icmiddle = find_ic_middle(icstart, icend, anchor_connection,
- acp, lp);
- ic = icup = icdown = icmiddle;
- if (debug)
- System.out.printf(" IC start = %d middle = %d end = %d\n",
- icstart, icmiddle, icend);
- done = false;
- direction = 0;
- while (!done) {
- if (direction < 0) {
- ic = icup;
- } else if (direction == 0) {
- ic = icmiddle;
- } else {
- ic = icdown;
- }
- if (ic >= 0) {
- cp = lp.getConnection(ic);
- if (anchor_connection == null || acp != cp) {
- if (direction == 0) {
- astart = cp.getAngle()
- - Math.asin(1.0 / 2.0 / radius);
- aend = cp.getAngle()
- + Math.asin(1.0 / 2.0 / radius);
- bases.get(cp.getStart()).setX(
- xc + radius * Math.cos(astart));
- bases.get(cp.getStart()).setY(
- yc + radius * Math.sin(astart));
- bases.get(cp.getEnd()).setX(
- xc + radius * Math.cos(aend));
- bases.get(cp.getEnd()).setY(
- yc + radius * Math.sin(aend));
- } else if (direction < 0) {
- j = ic + 1;
- if (j >= lp.getNconnection())
- j = 0;
- cp = lp.getConnection(ic);
- cpnext = lp.getConnection(j);
- cpx = cp.getXrad();
- cpy = cp.getYrad();
- ac = (cp.getAngle() + cpnext.getAngle()) / 2.0;
- if (cp.getAngle() > cpnext.getAngle())
- ac -= Math.PI;
- cnx = Math.cos(ac);
- cny = Math.sin(ac);
- lnx = cny;
- lny = -cnx;
- da = cpnext.getAngle() - cp.getAngle();
- if (da < 0.0)
- da += 2 * Math.PI;
- if (cp.isExtruded()) {
- if (da <= Math.PI / 2)
- rl = 2.0;
- else
- rl = 1.5;
- } else {
- rl = 1.0;
- }
- bases.get(cp.getEnd()).setX(
- bases.get(cpnext.getStart()).getX()
- + rl * lnx);
- bases.get(cp.getEnd()).setY(
- bases.get(cpnext.getStart()).getY()
- + rl * lny);
- bases.get(cp.getStart()).setX(
- bases.get(cp.getEnd()).getX() + cpy);
- bases.get(cp.getStart()).setY(
- bases.get(cp.getEnd()).getY() - cpx);
- } else {
- j = ic - 1;
- if (j < 0)
- j = lp.getNconnection() - 1;
- cp = lp.getConnection(j);
- cpnext = lp.getConnection(ic);
- cpnextx = cpnext.getXrad();
- cpnexty = cpnext.getYrad();
- ac = (cp.getAngle() + cpnext.getAngle()) / 2.0;
- if (cp.getAngle() > cpnext.getAngle())
- ac -= Math.PI;
- cnx = Math.cos(ac);
- cny = Math.sin(ac);
- lnx = -cny;
- lny = cnx;
- da = cpnext.getAngle() - cp.getAngle();
- if (da < 0.0)
- da += 2 * Math.PI;
- if (cp.isExtruded()) {
- if (da <= Math.PI / 2)
- rl = 2.0;
- else
- rl = 1.5;
- } else {
- rl = 1.0;
- }
- bases.get(cpnext.getStart()).setX(
- bases.get(cp.getEnd()).getX() + rl
- * lnx);
- bases.get(cpnext.getStart()).setY(
- bases.get(cp.getEnd()).getY() + rl
- * lny);
- bases.get(cpnext.getEnd()).setX(
- bases.get(cpnext.getStart()).getX()
- - cpnexty);
- bases.get(cpnext.getEnd()).setY(
- bases.get(cpnext.getStart()).getY()
- + cpnextx);
- }
- }
- }
- if (direction < 0) {
- if (icdown == icend) {
- icdown = -1;
- } else if (icdown >= 0) {
- if (++icdown >= lp.getNconnection()) {
- icdown = 0;
- }
- }
- direction = 1;
- } else {
- if (icup == icstart)
- icup = -1;
- else if (icup >= 0) {
- if (--icup < 0) {
- icup = lp.getNconnection() - 1;
- }
- }
- direction = -1;
- }
- done = icup == -1 && icdown == -1;
- }
- icnext = icend + 1;
- if (icnext >= lp.getNconnection())
- icnext = 0;
- if (icend != icstart
- && (!(icstart == icstart1 && icnext == icstart1))) {
-
- // Move the bases just constructed (or the radius) so that
- // the bisector of the end points is radius distance away
- // from the loop center.
-
- cp = lp.getConnection(icstart);
- cpnext = lp.getConnection(icend);
- dx = bases.get(cpnext.getEnd()).getX()
- - bases.get(cp.getStart()).getX();
- dy = bases.get(cpnext.getEnd()).getY()
- - bases.get(cp.getStart()).getY();
- midx = bases.get(cp.getStart()).getX() + dx / 2.0;
- midy = bases.get(cp.getStart()).getY() + dy / 2.0;
- rr = Math.sqrt(dx * dx + dy * dy);
- mx = dx / rr;
- my = dy / rr;
- vx = xc - midx;
- vy = yc - midy;
- rr = Math.sqrt(dx * dx + dy * dy);
- vx /= rr;
- vy /= rr;
- dotmv = vx * mx + vy * my;
- nrx = dotmv * mx - vx;
- nry = dotmv * my - vy;
- rr = Math.sqrt(nrx * nrx + nry * nry);
- nrx /= rr;
- nry /= rr;
-
- // Determine which side of the bisector the center should
- // be.
-
- dx = bases.get(cp.getStart()).getX() - xc;
- dy = bases.get(cp.getStart()).getY() - yc;
- ac = Math.atan2(dy, dx);
- if (ac < 0.0)
- ac += 2 * Math.PI;
- dx = bases.get(cpnext.getEnd()).getX() - xc;
- dy = bases.get(cpnext.getEnd()).getY() - yc;
- acn = Math.atan2(dy, dx);
- if (acn < 0.0)
- acn += 2 * Math.PI;
- if (acn < ac)
- acn += 2 * Math.PI;
- if (acn - ac > Math.PI)
- sign = -1;
- else
- sign = 1;
- nmidx = xc + sign * radius * nrx;
- nmidy = yc + sign * radius * nry;
- if (rooted) {
- xc -= nmidx - midx;
- yc -= nmidy - midy;
- } else {
- for (ic = icstart;;) {
- cp = lp.getConnection(ic);
- i = cp.getStart();
- bases.get(i).setX(
- bases.get(i).getX() + nmidx - midx);
- bases.get(i).setY(
- bases.get(i).getY() + nmidy - midy);
- i = cp.getEnd();
- bases.get(i).setX(
- bases.get(i).getX() + nmidx - midx);
- bases.get(i).setY(
- bases.get(i).getY() + nmidy - midy);
- if (ic == icend)
- break;
- if (++ic >= lp.getNconnection())
- ic = 0;
- }
- }
- }
- icstart = icnext;
- done_all_connections = icstart == icstart1;
- }
- for (ic = 0; ic < lp.getNconnection(); ic++) {
- cp = lp.getConnection(ic);
- j = ic + 1;
- if (j >= lp.getNconnection())
- j = 0;
- cpnext = lp.getConnection(j);
- dx = bases.get(cp.getEnd()).getX() - xc;
- dy = bases.get(cp.getEnd()).getY() - yc;
- rc = Math.sqrt(dx * dx + dy * dy);
- ac = Math.atan2(dy, dx);
- if (ac < 0.0)
- ac += 2 * Math.PI;
- dx = bases.get(cpnext.getStart()).getX() - xc;
- dy = bases.get(cpnext.getStart()).getY() - yc;
- rcn = Math.sqrt(dx * dx + dy * dy);
- acn = Math.atan2(dy, dx);
- if (acn < 0.0)
- acn += 2 * Math.PI;
- if (acn < ac)
- acn += 2 * Math.PI;
- dan = acn - ac;
- dcp = cpnext.getAngle() - cp.getAngle();
- if (dcp <= 0.0)
- dcp += 2 * Math.PI;
- if (Math.abs(dan - dcp) > Math.PI) {
- if (cp.isExtruded()) {
- warningEmition("Warning from traverse_loop. Loop "
- + lp.getNumber() + " has crossed regions\n");
- } else if ((cpnext.getStart() - cp.getEnd()) != 1) {
- cp.setExtruded(true);
- continue set_radius; // remplacement du goto
- }
- }
- if (cp.isExtruded()) {
- construct_extruded_segment(cp, cpnext);
- } else {
- n = cpnext.getStart() - cp.getEnd();
- if (n < 0)
- n += nbase + 1;
- angleinc = dan / n;
- for (j = 1; j < n; j++) {
- i = cp.getEnd() + j;
- if (i > nbase)
- i -= nbase + 1;
- a = ac + j * angleinc;
- rr = rc + (rcn - rc) * (a - ac) / dan;
- bases.get(i).setX(xc + rr * Math.cos(a));
- bases.get(i).setY(yc + rr * Math.sin(a));
- }
- }
- }
- break;
- }
- for (ic = 0; ic < lp.getNconnection(); ic++) {
- if (icroot != ic) {
- cp = lp.getConnection(ic);
- generate_region(cp);
- traverse_loop(cp.getLoop(), cp);
- }
- }
- n = 0;
- sx = 0.0;
- sy = 0.0;
- for (ic = 0; ic < lp.getNconnection(); ic++) {
- j = ic + 1;
- if (j >= lp.getNconnection())
- j = 0;
- cp = lp.getConnection(ic);
- cpnext = lp.getConnection(j);
- n += 2;
- sx += bases.get(cp.getStart()).getX()
- + bases.get(cp.getEnd()).getX();
- sy += bases.get(cp.getStart()).getY()
- + bases.get(cp.getEnd()).getY();
- if (!cp.isExtruded()) {
- for (j = cp.getEnd() + 1; j != cpnext.getStart(); j++) {
- if (j > nbase)
- j -= nbase + 1;
- n++;
- sx += bases.get(j).getX();
- sy += bases.get(j).getY();
- }
- }
- }
- lp.setX(sx / n);
- lp.setY(sy / n);
- }
-
- /**
- * For the loop pointed to by lp, determine the radius of the loop that will
- * ensure that each base around the loop will have a separation of at least
- * lencut around the circle. If a segment joining two connectors will not
- * support this separation, then the flag, extruded, will be set in the
- * first of these two indicators. The radius is set in lp.
- *
- * The radius is selected by a least squares procedure where the sum of the
- * squares of the deviations of length from the ideal value of 1 is used as
- * the error function.
- */
- private void determine_radius(Loop lp, double lencut) {
- if (debug)
- System.out.println(" Determine_radius");
- double mindit, ci, dt, sumn, sumd, radius, dit;
- int i, j, end, start, imindit = 0;
- Connection cp = new Connection(), cpnext = new Connection();
- double rt2_2 = 0.7071068;
-
- do {
- mindit = 1.0e10;
- for (sumd = 0.0, sumn = 0.0, i = 0; i < lp.getNconnection(); i++) {
- cp = lp.getConnection(i);
- j = i + 1;
- if (j >= lp.getNconnection())
- j = 0;
- cpnext = lp.getConnection(j);
- end = cp.getEnd();
- start = cpnext.getStart();
- if (start < end)
- start += nbase + 1;
- dt = cpnext.getAngle() - cp.getAngle();
- if (dt <= 0.0)
- dt += 2 * Math.PI;
- if (!cp.isExtruded())
- ci = start - end;
- else {
- if (dt <= Math.PI / 2)
- ci = 2.0;
- else
- ci = 1.5;
- }
- sumn += dt * (1.0 / ci + 1.0);
- sumd += dt * dt / ci;
- dit = dt / ci;
- if (dit < mindit && !cp.isExtruded() && ci > 1.0) {
- mindit = dit;
- imindit = i;
- }
- }
- radius = sumn / sumd;
- if (radius < rt2_2)
- radius = rt2_2;
- if (mindit * radius < lencut) {
- lp.getConnection(imindit).setExtruded(true);
- }
- } while (mindit * radius < lencut);
- if (lp.getRadius() > 0.0)
- radius = lp.getRadius();
- else
- lp.setRadius(radius);
- }
-
- /**
- * Determines if the connections cp and cpnext are connected
- */
- private boolean connected_connection(Connection cp, Connection cpnext) {
- if (debug)
- System.out.println(" Connected_connection");
- if (cp.isExtruded()) {
- return true;
- } else if (cp.getEnd() + 1 == cpnext.getStart()) {
- return true;
- } else {
- return false;
- }
- }
-
- /**
- * Finds the middle of a set of connected connectors. This is normally the
- * middle connection in the sequence except if one of the connections is the
- * anchor, in which case that connection will be used.
- *
- * @throws ExceptionNAViewAlgorithm
- */
- private int find_ic_middle(int icstart, int icend,
- Connection anchor_connection, Connection acp, Loop lp)
- throws ExceptionNAViewAlgorithm {
- if (debug)
- System.out.println(" Find_ic_middle");
- int count, ret, ic, i;
- boolean done;
-
- count = 0;
- ret = -1;
- ic = icstart;
- done = false;
- while (!done) {
- if (count++ > lp.getNconnection() * 2) {
- throw new ExceptionNAViewAlgorithm(
- "Infinite loop detected in find_ic_middle");
- }
- if (anchor_connection != null && lp.getConnection(ic) == acp) {
- ret = ic;
- }
- done = ic == icend;
- if (++ic >= lp.getNconnection()) {
- ic = 0;
- }
- }
- if (ret == -1) {
- for (i = 1, ic = icstart; i < (count + 1) / 2; i++) {
- if (++ic >= lp.getNconnection())
- ic = 0;
- }
- ret = ic;
- }
- return ret;
- }
-
- /**
- * Generates the coordinates for the base pairing region of a connection
- * given the position of the starting base pair.
- *
- * @throws ExceptionNAViewAlgorithm
- */
- private void generate_region(Connection cp) throws ExceptionNAViewAlgorithm {
- if (debug)
- System.out.println(" Generate_region");
- int l, start, end, i, mate;
- Region rp;
-
- rp = cp.getRegion();
- l = 0;
- if (cp.getStart() == rp.getStart1()) {
- start = rp.getStart1();
- end = rp.getEnd1();
- } else {
- start = rp.getStart2();
- end = rp.getEnd2();
- }
- if (bases.get(cp.getStart()).getX() > ANUM - 100.0
- || bases.get(cp.getEnd()).getX() > ANUM - 100.0) {
- throw new ExceptionNAViewAlgorithm(
- "Bad region passed to generate_region. Coordinates not defined.");
- }
- for (i = start + 1; i <= end; i++) {
- l++;
- bases.get(i).setX(
- bases.get(cp.getStart()).getX() + HELIX_FACTOR * l
- * cp.getXrad());
- bases.get(i).setY(
- bases.get(cp.getStart()).getY() + HELIX_FACTOR * l
- * cp.getYrad());
- mate = bases.get(i).getMate();
- bases.get(mate).setX(
- bases.get(cp.getEnd()).getX() + HELIX_FACTOR * l
- * cp.getXrad());
- bases.get(mate).setY(
- bases.get(cp.getEnd()).getY() + HELIX_FACTOR * l
- * cp.getYrad());
-
- }
- }
-
- /**
- * Draws the segment of residue between the bases numbered start through
- * end, where start and end are presumed to be part of a base pairing
- * region. They are drawn as a circle which has a chord given by the ends of
- * two base pairing regions defined by the connections.
- *
- * @throws ExceptionNAViewAlgorithm
- */
- private void construct_circle_segment(int start, int end)
- throws ExceptionNAViewAlgorithm {
- if (debug)
- System.out.println(" Construct_circle_segment");
- double dx, dy, rr, midx, midy, xn, yn, nrx, nry, mx, my, a;
- int l, j, i;
-
- dx = bases.get(end).getX() - bases.get(start).getX();
- dy = bases.get(end).getY() - bases.get(start).getY();
- rr = Math.sqrt(dx * dx + dy * dy);
- l = end - start;
- if (l < 0)
- l += nbase + 1;
- if (rr >= l) {
- dx /= rr;
- dy /= rr;
- for (j = 1; j < l; j++) {
- i = start + j;
- if (i > nbase)
- i -= nbase + 1;
- bases.get(i).setX(
- bases.get(start).getX() + dx * (double) j / (double) l);
- bases.get(i).setY(
- bases.get(start).getY() + dy * (double) j / (double) l);
- }
- } else {
- find_center_for_arc((l - 1), rr);
- dx /= rr;
- dy /= rr;
- midx = bases.get(start).getX() + dx * rr / 2.0;
- midy = bases.get(start).getY() + dy * rr / 2.0;
- xn = dy;
- yn = -dx;
- nrx = midx + _h * xn;
- nry = midy + _h * yn;
- mx = bases.get(start).getX() - nrx;
- my = bases.get(start).getY() - nry;
- rr = Math.sqrt(mx * mx + my * my);
- a = Math.atan2(my, mx);
- for (j = 1; j < l; j++) {
- i = start + j;
- if (i > nbase)
- i -= nbase + 1;
- bases.get(i).setX(nrx + rr * Math.cos(a + j * angleinc));
- bases.get(i).setY(nry + rr * Math.sin(a + j * angleinc));
- }
- }
- }
-
- /**
- * Constructs the segment between cp and cpnext as a circle if possible.
- * However, if the segment is too large, the lines are drawn between the two
- * connecting regions, and bases are placed there until the connecting
- * circle will fit.
- *
- * @throws ExceptionNAViewAlgorithm
- */
- private void construct_extruded_segment(Connection cp, Connection cpnext)
- throws ExceptionNAViewAlgorithm {
- if (debug)
- System.out.println(" Construct_extruded_segment");
- double astart, aend1, aend2, aave, dx, dy, a1, a2, ac, rr, da, dac;
- int start, end, n, nstart, nend;
- boolean collision;
-
- astart = cp.getAngle();
- aend2 = aend1 = cpnext.getAngle();
- if (aend2 < astart)
- aend2 += 2 * Math.PI;
- aave = (astart + aend2) / 2.0;
- start = cp.getEnd();
- end = cpnext.getStart();
- n = end - start;
- if (n < 0)
- n += nbase + 1;
- da = cpnext.getAngle() - cp.getAngle();
- if (da < 0.0) {
- da += 2 * Math.PI;
- }
- if (n == 2)
- construct_circle_segment(start, end);
- else {
- dx = bases.get(end).getX() - bases.get(start).getX();
- dy = bases.get(end).getY() - bases.get(start).getY();
- rr = Math.sqrt(dx * dx + dy * dy);
- dx /= rr;
- dy /= rr;
- if (rr >= 1.5 && da <= Math.PI / 2) {
- nstart = start + 1;
- if (nstart > nbase)
- nstart -= nbase + 1;
- nend = end - 1;
- if (nend < 0)
- nend += nbase + 1;
- bases.get(nstart).setX(bases.get(start).getX() + 0.5 * dx);
- bases.get(nstart).setY(bases.get(start).getY() + 0.5 * dy);
- bases.get(nend).setX(bases.get(end).getX() - 0.5 * dx);
- bases.get(nend).setY(bases.get(end).getY() - 0.5 * dy);
- start = nstart;
- end = nend;
- }
- do {
- collision = false;
- construct_circle_segment(start, end);
- nstart = start + 1;
- if (nstart > nbase)
- nstart -= nbase + 1;
- dx = bases.get(nstart).getX() - bases.get(start).getX();
- dy = bases.get(nstart).getY() - bases.get(start).getY();
- a1 = Math.atan2(dy, dx);
- if (a1 < 0.0)
- a1 += 2 * Math.PI;
- dac = a1 - astart;
- if (dac < 0.0)
- dac += 2 * Math.PI;
- if (dac > Math.PI)
- collision = true;
- nend = end - 1;
- if (nend < 0)
- nend += nbase + 1;
- dx = bases.get(nend).getX() - bases.get(end).getX();
- dy = bases.get(nend).getY() - bases.get(end).getY();
- a2 = Math.atan2(dy, dx);
- if (a2 < 0.0)
- a2 += 2 * Math.PI;
- dac = aend1 - a2;
- if (dac < 0.0)
- dac += 2 * Math.PI;
- if (dac > Math.PI)
- collision = true;
- if (collision) {
- ac = minf2(aave, astart + 0.5);
- bases.get(nstart).setX(
- bases.get(start).getX() + Math.cos(ac));
- bases.get(nstart).setY(
- bases.get(start).getY() + Math.sin(ac));
- start = nstart;
- ac = maxf2(aave, aend2 - 0.5);
- bases.get(nend).setX(bases.get(end).getX() + Math.cos(ac));
- bases.get(nend).setY(bases.get(end).getY() + Math.sin(ac));
- end = nend;
- n -= 2;
- }
- } while (collision && n > 1);
- }
- }
-
- /**
- * Given n points to be placed equidistantly and equiangularly on a polygon
- * which has a chord of length, b, find the distance, h, from the midpoint
- * of the chord for the center of polygon. Positive values mean the center
- * is within the polygon and the chord, whereas negative values mean the
- * center is outside the chord. Also, the radial angle for each polygon side
- * is returned in theta.
- *
- * The procedure uses a bisection algorithm to find the correct value for
- * the center. Two equations are solved, the angles around the center must
- * add to 2*Math.PI, and the sides of the polygon excluding the chord must
- * have a length of 1.
- *
- * @throws ExceptionNAViewAlgorithm
- */
- private void find_center_for_arc(double n, double b)
- throws ExceptionNAViewAlgorithm {
- if (debug)
- System.out.println(" Find_center_for_arc");
- double h, hhi, hlow, r, disc, theta, e, phi;
- int iter;
-
- hhi = (n + 1.0) / Math.PI;
- // changed to prevent div by zero if (ih)
- hlow = -hhi - b / (n + 1.000001 - b);
- if (b < 1)
- // otherwise we might fail below (ih)
- hlow = 0;
- iter = 0;
- do {
- h = (hhi + hlow) / 2.0;
- r = Math.sqrt(h * h + b * b / 4.0);
- // if (r<0.5) {r = 0.5; h = 0.5*Math.sqrt(1-b*b);}
- disc = 1.0 - 0.5 / (r * r);
- if (Math.abs(disc) > 1.0) {
- throw new ExceptionNAViewAlgorithm(
- "Unexpected large magnitude discriminant = " + disc
- + " " + r);
- }
- theta = Math.acos(disc);
- // theta = 2*Math.acos(Math.sqrt(1-1/(4*r*r)));
- phi = Math.acos(h / r);
- e = theta * (n + 1) + 2 * phi - 2 * Math.PI;
- if (e > 0.0) {
- hlow = h;
- } else {
- hhi = h;
- }
- } while (Math.abs(e) > 0.0001 && ++iter < MAXITER);
- if (iter >= MAXITER) {
- if (noIterationFailureYet) {
- warningEmition("Iteration failed in find_center_for_arc");
- noIterationFailureYet = false;
- }
- h = 0.0;
- theta = 0.0;
- }
- _h = h;
- angleinc = theta;
- }
-
- private double minf2(double x1, double x2) {
- return ((x1) < (x2)) ? (x1) : (x2);
- }
-
- private double maxf2(double x1, double x2) {
- return ((x1) > (x2)) ? (x1) : (x2);
- }
-
- public void warningEmition(String warningMessage) throws ExceptionNAViewAlgorithm {
- throw (new ExceptionNAViewAlgorithm(warningMessage));
- }
-}
git://source.jalview.org / jalview.git / blobdiff