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java.lang.Objectfr.orsay.lri.varna.models.naView.NAView
public class NAView
Field Summary | |
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private double |
_h
|
private ArrayList<InterfaceVARNAListener> |
_listeVARNAListener
|
private double |
angleinc
|
private double |
ANUM
|
(package private) double |
BACKBONE_DISTANCE
|
private ArrayList<Base> |
bases
|
private boolean |
debug
|
(package private) double |
HELIX_FACTOR
|
private double |
lencut
|
private int |
loop_count
|
private ArrayList<Loop> |
loops
|
private int |
MAXITER
|
private int |
nbase
|
private boolean |
noIterationFailureYet
|
private int |
nregion
|
private double |
RADIUS_REDUCTION_FACTOR
|
private ArrayList<Region> |
regions
|
private Radloop |
rlphead
|
private Loop |
root
|
Constructor Summary | |
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NAView()
|
Method Summary | |
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private boolean |
connected_connection(Connection cp,
Connection cpnext)
Determines if the connections cp and cpnext are connected |
private void |
construct_circle_segment(int start,
int end)
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. |
private void |
construct_extruded_segment(Connection cp,
Connection cpnext)
Constructs the segment between cp and cpnext as a circle if possible. |
private Loop |
construct_loop(int ibase)
Starting at residue ibase, recursively constructs the loop containing said base and all deeper bases. |
private int |
depth(Loop lp)
Determines the depth of loop, lp. |
private void |
determine_depths()
Determine the depth of all loops. |
private void |
determine_radius(Loop lp,
double lencut)
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. |
private void |
dump_loops()
Displays all the loops. |
private void |
find_center_for_arc(double n,
double b)
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. |
private void |
find_central_loop()
Find node of greatest branching that is deepest. |
private int |
find_ic_middle(int icstart,
int icend,
Connection anchor_connection,
Connection acp,
Loop lp)
Finds the middle of a set of connected connectors. |
private void |
find_regions()
Identifies the regions in the structure. |
private void |
generate_region(Connection cp)
Generates the coordinates for the base pairing region of a connection given the position of the starting base pair. |
private void |
infoBasesExtracted()
|
private void |
infoBasesMate()
|
private void |
infoRegions()
|
private void |
infoRoot()
|
private void |
infoStructure(ArrayList<Integer> pair_table)
|
private double |
maxf2(double x1,
double x2)
|
private double |
minf2(double x1,
double x2)
|
int |
naview_xy_coordinates(ArrayList<Short> pair_table2,
ArrayList<Double> x,
ArrayList<Double> y)
|
private void |
read_in_bases(ArrayList<Integer> pair_table)
|
private void |
traverse_loop(Loop lp,
Connection anchor_connection)
This is the workhorse of the display program. |
void |
warningEmition(String warningMessage)
|
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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private final double ANUM
private final int MAXITER
private ArrayList<Base> bases
private int nbase
private int nregion
private int loop_count
private Loop root
private ArrayList<Loop> loops
private ArrayList<Region> regions
private Radloop rlphead
private double lencut
private final double RADIUS_REDUCTION_FACTOR
private boolean debug
private double angleinc
private double _h
private ArrayList<InterfaceVARNAListener> _listeVARNAListener
private boolean noIterationFailureYet
double HELIX_FACTOR
double BACKBONE_DISTANCE
Constructor Detail |
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public NAView()
Method Detail |
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public int naview_xy_coordinates(ArrayList<Short> pair_table2, ArrayList<Double> x, ArrayList<Double> y) throws fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm
fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm
private void infoStructure(ArrayList<Integer> pair_table)
private void infoBasesMate()
private void infoRegions()
private void infoBasesExtracted()
private void infoRoot()
private void read_in_bases(ArrayList<Integer> pair_table)
private void find_regions()
private Loop construct_loop(int ibase) throws fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm
fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm
private void dump_loops()
private void find_central_loop()
private void determine_depths()
private int depth(Loop lp)
private void traverse_loop(Loop lp, Connection anchor_connection) throws fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm
fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm
private void determine_radius(Loop lp, double lencut)
private boolean connected_connection(Connection cp, Connection cpnext)
private int find_ic_middle(int icstart, int icend, Connection anchor_connection, Connection acp, Loop lp) throws fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm
fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm
private void generate_region(Connection cp) throws fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm
fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm
private void construct_circle_segment(int start, int end) throws fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm
fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm
private void construct_extruded_segment(Connection cp, Connection cpnext) throws fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm
fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm
private void find_center_for_arc(double n, double b) throws fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm
fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm
private double minf2(double x1, double x2)
private double maxf2(double x1, double x2)
public void warningEmition(String warningMessage) throws fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm
fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm
|
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