/**
 * Created with IntelliJ IDEA.
 * User: rebeccamancy
 * Date: 22/01/2013
 * Time: 15:11
 * To change this template use File | Settings | File Templates.
 */
public class Ecology {
    private Habitat hab;
    private Model mod;
    private double lambdaM;
    private double[] x2Vi, xyVi;
    private int maxViPatch;
    private double[][] matC;
    private double[] vecE;
    private QSD qsd;

    /**
     * Constructor - uses hab and mod to create an Ecology object
     * @param hab
     * @param mod
     */
    public Ecology (Habitat hab, Model mod) {
        this.hab = hab;
        this.mod = mod;
        int numPatches = hab.getNumPatches();
        matC = new double[numPatches][numPatches];
        vecE = new double[numPatches];

        // Construct matC (colonisation rates)
        for (int to=0; to < numPatches; to++) {
            for (int from=0; from < numPatches; from++) {
                if (from==to) {
                    matC[to][from] = 0; // no self-colonisation
                } else {
                    matC[to][from] = mod.contribRate(hab, from, to);
                }
            }
        }
        // Construct vecE (extinction rates)
        for (int from=0; from < numPatches; from++) {
            vecE[from] = mod.extRate(hab, from, 1);  // todo - 1 here refers to the to site which is irrelevant
        }

        M matM = new M(hab, mod);
        lambdaM = matM.getLambda();
        x2Vi = matM.getNorx2Vi();
        xyVi = matM.getNorxyVi();
        maxViPatch = matM.getMaxViPatch();
    }

    /**
     * Sets the QSD attribute given a qsd object
     * @param qsd
     */
    public void setQsd(QSD qsd) {
        this.qsd = qsd;
    }

    public QSD getQsd() {
        return this.qsd;
    }

    public String getMetrics() {
        return lambdaM + "," + x2Vi.toString() + "," + xyVi.toString();
    }

    public double getLambdaM() {
        return lambdaM;
    }

    public double getx2Vi(int patchID) {
        return x2Vi[patchID];
    }

    public double getxyVi(int patchID) {
        return xyVi[patchID];
    }

    public int getMaxViPatch() {
        return maxViPatch;
    }

    public Habitat getHab() {
        return hab;
    }

    public Model getMod() {
        return mod;
    }

    /**
     * Calculates transition rate for a particular focal patch, given other patch status (and using matC, vecE)
     * @param focalPatch     the patch whose rates we're calculating
     * @param patchStatus    status of all other patches
     * @return
     */
    public double calcRate(int focalPatch, int[] patchStatus) {
        double r = 0;
        if (patchStatus[focalPatch] == 1) {    // patch is alive so transition rate is just extinction rate
            r = vecE[focalPatch];
        } else {
            for (int fromPatch=0; fromPatch<patchStatus.length; fromPatch++) {   // patch dead so transitions according to sum of colon rates of all other patches
                if ((fromPatch != focalPatch) && (patchStatus[fromPatch] == 1)) {   // don't add in anything from dead patches or self
                    r = r + matC[focalPatch][fromPatch];
                }
            }
        }
        return r;
    }

    /**
     * Converts ecology to string representing matrix of colonisation rates, and below extinction rates (row), for csv
     * @return   string formatted as csv to be read into a single matrix in Matlab
     */
    public String toString() {
        // Construct String for matrix C
        String strMatC = ""; String strVecE = "";
        for (int to=0; to < hab.getNumPatches(); to++) {      // from on as go along
            for (int from=0; from < hab.getNumPatches(); from++) {        // to as go down
                if (from > 0) {
                    strMatC += ", ";
                }
                strMatC += matC[to][from];
            }
            strMatC += "\n";
        }
        // Construct String for vector E
        for (int from=0; from < hab.getNumPatches(); from++) {
            if (from > 0) {
                strVecE += ", ";
            }
            strVecE += vecE[from];
        }
        strVecE += "\n";

        return strMatC + strVecE;
    }
}