/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 * Created on Mar 9, 2010
 * Author: Spencer Bliven
 *
 */

package org.biojava.nbio.structure.align.ce;


import org.biojava.nbio.structure.*;
import org.biojava.nbio.structure.align.model.AFPChain;
import org.biojava.nbio.structure.align.util.AFPAlignmentDisplay;
import org.biojava.nbio.structure.align.util.ConfigurationException;
import org.biojava.nbio.structure.geometry.Matrices;
import org.biojava.nbio.structure.geometry.SuperPositions;
import org.biojava.nbio.structure.jama.Matrix;

import java.lang.reflect.InvocationTargetException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

import javax.vecmath.Matrix4d;

/**
 * A wrapper for {@link CeMain} which sets default parameters to be appropriate for finding
 * circular permutations.
 * <p>
 * A circular permutation consists of a single cleavage point and rearrangement
 * between two structures, for example:
 * <pre>
 * ABCDEFG
 * DEFGABC
 * </pre>
 * @author Spencer Bliven.
 *
 */
public class CeCPMain extends CeMain {
        private static boolean debug = false;

        public static final String algorithmName = "jCE Circular Permutation";

        /**
         *  version history:
         *  1.5 - Added more parameters to the command line, including -maxOptRMSD
         *  1.4 - Added DuplicationHint parameter & default to duplicating the shorter chain
         *  1.3 - Short CPs are now discarded
         *  1.2 - now supports check AlignmentTools.isSequentialAlignment. XML protocol
         *  1.1 - skipped, (trying to avoid confusion with jfatcat in all vs. all comparisons)
         *  1.0 - initial release
         */
        public static final String version = "1.5";

        public CeCPMain(){
                super();
                params = new CECPParameters();
        }

        @Override
        public String getAlgorithmName() {
                return CeCPMain.algorithmName;
        }

        @Override
        public String getVersion() {
                return CeCPMain.version;
        }

        public static void main(String[] args) throws ConfigurationException {
                CeCPUserArgumentProcessor processor = new CeCPUserArgumentProcessor(); //Responsible for creating a CeCPMain instance
                processor.process(args);
        }


        /**
         * Aligns ca1 and ca2 using a heuristic to check for CPs.
         * <p>
         * Aligns ca1 against a doubled ca2, then cleans up the alignment.
         * @param ca1
         * @param ca2
         * @param param
         * @return the alignment, possibly containing a CP.
         * @throws StructureException
         */
        @Override
        public AFPChain align(Atom[] ca1, Atom[] ca2, Object param) throws StructureException{
                if ( ! (param instanceof CECPParameters))
                        throw new IllegalArgumentException("CE algorithm needs an object of call CeParameters as argument.");

                CECPParameters cpparams = (CECPParameters) param;
                this.params = cpparams;

                boolean duplicateRight;

                switch( cpparams.getDuplicationHint() ) {
                case LEFT:
                        duplicateRight = false;
                        break;
                case RIGHT:
                        duplicateRight = true;
                        break;
                case SHORTER:
                        duplicateRight = ca1.length >= ca2.length;
                        break;
                default:
                        duplicateRight = true;
                }


                if( duplicateRight ) {
                        return alignRight(ca1, ca2, cpparams);
                } else {
                        if(debug) {
                                System.out.println("Swapping alignment order.");
                        }
                        AFPChain afpChain = this.alignRight(ca2, ca1, cpparams);
                        return invertAlignment(afpChain);
                }
        }

        /**
         * Aligns the structures, duplicating ca2 regardless of
         * {@link CECPParameters.getDuplicationHint() param.getDuplicationHint}.
         * @param ca1
         * @param ca2
         * @param cpparams
         * @return
         * @throws StructureException
         */
        private AFPChain alignRight(Atom[] ca1, Atom[] ca2, CECPParameters cpparams)
                        throws StructureException {
                long startTime = System.currentTimeMillis();

                Atom[] ca2m = StructureTools.duplicateCA2(ca2);

                if(debug) {
                        System.out.format("Duplicating ca2 took %s ms\n",System.currentTimeMillis()-startTime);
                        startTime = System.currentTimeMillis();
                }

                // Do alignment
                AFPChain afpChain = super.align(ca1, ca2m,params);

                // since the process of creating ca2m strips the name info away, set it explicitely
                try {
                        afpChain.setName2(ca2[0].getGroup().getChain().getStructure().getName());
                } catch( Exception e) {}

                if(debug) {
                        System.out.format("Running %dx2*%d alignment took %s ms\n",ca1.length,ca2.length,System.currentTimeMillis()-startTime);
                        startTime = System.currentTimeMillis();
                }
                afpChain = postProcessAlignment(afpChain, ca1, ca2m, calculator, cpparams);

                if(debug) {
                        System.out.format("Finding CP point took %s ms\n",System.currentTimeMillis()-startTime);
                        startTime = System.currentTimeMillis();
                }

                return afpChain;
        }



        /** Circular permutation specific code to be run after the standard CE alignment
         *
         * @param afpChain The finished alignment
         * @param ca1 CA atoms of the first protein
         * @param ca2m A duplicated copy of the second protein
         * @param calculator The CECalculator used to create afpChain
         * @throws StructureException
         */
        public static AFPChain postProcessAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2m,CECalculator calculator ) throws StructureException{
                return postProcessAlignment(afpChain, ca1, ca2m, calculator, null);
        }

        /** Circular permutation specific code to be run after the standard CE alignment
         *
         * @param afpChain The finished alignment
         * @param ca1 CA atoms of the first protein
         * @param ca2m A duplicated copy of the second protein
         * @param calculator The CECalculator used to create afpChain
         * @param param Parameters
         * @throws StructureException
         */
        public static AFPChain postProcessAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2m,CECalculator calculator, CECPParameters param ) throws StructureException{

                // remove bottom half of the matrix
                Matrix doubledMatrix = afpChain.getDistanceMatrix();

                // the matrix can be null if the alignment is too short.
                if ( doubledMatrix != null ) {
                        assert(doubledMatrix.getRowDimension() == ca1.length);
                        assert(doubledMatrix.getColumnDimension() == ca2m.length);

                        Matrix singleMatrix = doubledMatrix.getMatrix(0, ca1.length-1, 0, (ca2m.length/2)-1);
                        assert(singleMatrix.getRowDimension() == ca1.length);
                        assert(singleMatrix.getColumnDimension() == (ca2m.length/2));

                        afpChain.setDistanceMatrix(singleMatrix);
                }
                // Check for circular permutations
                int alignLen = afpChain.getOptLength();
                if ( alignLen > 0) {
                        afpChain = filterDuplicateAFPs(afpChain,calculator,ca1,ca2m,param);
                }
                return afpChain;
        }

        /**
         * Swaps the order of structures in an AFPChain
         * @param a
         * @return
         */
        public AFPChain invertAlignment(AFPChain a) {
                String name1 = a.getName1();
                String name2 = a.getName2();
                a.setName1(name2);
                a.setName2(name1);

                int len1 = a.getCa1Length();
                a.setCa1Length( a.getCa2Length() );
                a.setCa2Length( len1 );

                int beg1 = a.getAlnbeg1();
                a.setAlnbeg1(a.getAlnbeg2());
                a.setAlnbeg2(beg1);

                char[] alnseq1 = a.getAlnseq1();
                a.setAlnseq1(a.getAlnseq2());
                a.setAlnseq2(alnseq1);

                Matrix distab1 = a.getDisTable1();
                a.setDisTable1(a.getDisTable2());
                a.setDisTable2(distab1);

                int[] focusRes1 = a.getFocusRes1();
                a.setFocusRes1(a.getFocusRes2());
                a.setFocusRes2(focusRes1);

                //What are aftIndex and befIndex used for? How are they indexed?
                //a.getAfpAftIndex()


                String[][][] pdbAln = a.getPdbAln();
                if( pdbAln != null) {
                        for(int block = 0; block < a.getBlockNum(); block++) {
                                String[] paln1 = pdbAln[block][0];
                                pdbAln[block][0] = pdbAln[block][1];
                                pdbAln[block][1] = paln1;
                        }
                }

                int[][][] optAln = a.getOptAln();
                if( optAln != null ) {
                        for(int block = 0; block < a.getBlockNum(); block++) {
                                int[] aln1 = optAln[block][0];
                                optAln[block][0] = optAln[block][1];
                                optAln[block][1] = aln1;
                        }
                }
                a.setOptAln(optAln); // triggers invalidate()

                Matrix distmat = a.getDistanceMatrix();
                if(distmat != null)
                        a.setDistanceMatrix(distmat.transpose());


                // invert the rotation matrices
                Matrix[] blockRotMat = a.getBlockRotationMatrix();
                Atom[] shiftVec = a.getBlockShiftVector();
                if( blockRotMat != null) {
                        for(int block = 0; block < a.getBlockNum(); block++) {
                                if(blockRotMat[block] != null) {
                                        // if y=x*A+b, then x=y*inv(A)-b*inv(A)
                                        blockRotMat[block] = blockRotMat[block].inverse();

                                        Calc.rotate(shiftVec[block],blockRotMat[block]);
                                        shiftVec[block] = Calc.invert(shiftVec[block]);
                                }
                        }
                }

                return a;
        }

        /**
         * Takes as input an AFPChain where ca2 has been artificially duplicated.
         * This raises the possibility that some residues of ca2 will appear in
         * multiple AFPs. This method filters out duplicates and makes sure that
         * all AFPs are numbered relative to the original ca2.
         *
         * <p>The current version chooses a CP site such that the length of the
         * alignment is maximized.
         *
         * <p>This method does <i>not</i> update scores to reflect the filtered alignment.
         * It <i>does</i> update the RMSD and superposition.
         *
         * @param afpChain The alignment between ca1 and ca2-ca2. Blindly assumes
         *  that ca2 has been duplicated.
         * @return A new AFPChain consisting of ca1 to ca2, with each residue in
         *  at most 1 AFP.
         * @throws StructureException
         */
        public static AFPChain filterDuplicateAFPs(AFPChain afpChain, CECalculator ceCalc, Atom[] ca1, Atom[] ca2duplicated) throws StructureException {
                return filterDuplicateAFPs(afpChain, ceCalc, ca1, ca2duplicated, null);
        }
        public static AFPChain filterDuplicateAFPs(AFPChain afpChain, CECalculator ceCalc,
                        Atom[] ca1, Atom[] ca2duplicated, CECPParameters params) throws StructureException {
                AFPChain newAFPChain = new AFPChain(afpChain);

                if(params == null)
                        params = new CECPParameters();

                final int minCPlength = params.getMinCPLength();


                int ca2len = afpChain.getCa2Length()/2;
                newAFPChain.setCa2Length(ca2len);

                // Fix optimal alignment
                int[][][] optAln = afpChain.getOptAln();
                int[] optLen = afpChain.getOptLen();
                int alignLen = afpChain.getOptLength();
                if (alignLen < 1) return newAFPChain;

                assert(afpChain.getBlockNum() == 1); // Assume that CE returns just one block


                // Determine the region where ca2 and ca2' overlap

                // The bounds of the alignment wrt ca2-ca2'
                int nStart = optAln[0][1][0]; //alignment N-terminal
                int cEnd = optAln[0][1][alignLen-1]; // alignment C-terminal
                // overlap is between nStart and cEnd


                int firstRes = nStart; // start res number after trimming
                int lastRes = nStart+ca2len;  // last res number after trimming
                if(nStart >= ca2len || cEnd < ca2len) { // no circular permutation
                        firstRes=nStart;
                        lastRes=cEnd;
                } else {
                        // Rule: maximize the length of the alignment

                        int overlapLength = cEnd+1 - nStart - ca2len;
                        if(overlapLength <= 0) {
                                // no overlap!

                                CPRange minCP = calculateMinCP(optAln[0][1], alignLen, ca2len, minCPlength);

                                firstRes=nStart;
                                lastRes=cEnd;

                                // Remove short blocks
                                if(firstRes > minCP.n) {
                                        firstRes = ca2len;

                                        if(debug) {
                                                System.out.format("Discarding n-terminal block as too " +
                                                                "short (%d residues, needs %d)\n",
                                                                minCP.mid, minCPlength);
                                        }
                                }

                                if(lastRes < minCP.c) {
                                        lastRes = ca2len-1;

                                        if(debug) {
                                                System.out.format("Discarding c-terminal block as too " +
                                                                "short (%d residues, needs %d)\n",
                                                                optLen[0] - minCP.mid, minCPlength);
                                        }
                                }

                        }
                        else {
                                // overlap!

                                CutPoint cp = calculateCutPoint(optAln[0][1], nStart, cEnd,
                                                overlapLength, alignLen, minCPlength, ca2len, firstRes);

                                // Adjust alignment length for trimming
                                //alignLen -= cp.numResiduesCut; //TODO inaccurate

                                firstRes = cp.firstRes;
                                lastRes = cp.lastRes;

                                //TODO Now have CP site, and could do a NxM alignment for further optimization.
                                // For now, does not appear to be worth the 50% increase in time

                                //TODO Bug: scores need to be recalculated
                        }
                }



                // Fix numbering:
                // First, split up the atoms into left and right blocks
                List< ResiduePair > left = new ArrayList<ResiduePair>(); // residues from left of duplication
                List< ResiduePair > right = new ArrayList<ResiduePair>(); // residues from right of duplication

                for(int i=0;i<optLen[0];i++) {
                        if( optAln[0][1][i] >= firstRes && optAln[0][1][i] <= lastRes ) { // not trimmed
                                if(optAln[0][1][i] < ca2len) { // in first half of ca2
                                        left.add(new ResiduePair(optAln[0][0][i],optAln[0][1][i]));
                                }
                                else {
                                        right.add(new ResiduePair(optAln[0][0][i],optAln[0][1][i]-ca2len));
                                }
                        }
                }
                //assert(left.size()+right.size() == alignLen);
                alignLen = 0;

                // Now we don't care about left/right, so just call them "blocks"
                List<List<ResiduePair>> blocks = new ArrayList<List<ResiduePair>>(2);
                if( !left.isEmpty() ) {
                        blocks.add(left);
                        alignLen += left.size();
                }
                if( !right.isEmpty()) {
                        blocks.add(right);
                        alignLen += right.size();
                }
                left=null; right = null;

                // Put the blocks back together into arrays for the AFPChain
                int[][][] newAlign = new int[blocks.size()][][];
                int[] blockLengths = new int[blocks.size()];
                for(int blockNum = 0; blockNum < blocks.size(); blockNum++) {
                        //Alignment
                        List<ResiduePair> block = blocks.get(blockNum);
                        newAlign[blockNum] = new int[2][block.size()];
                        for(int i=0;i<block.size();i++) {
                                ResiduePair pair = block.get(i);
                                newAlign[blockNum][0][i] = pair.a;
                                newAlign[blockNum][1][i] = pair.b;
                        }

                        // Block lengths
                        blockLengths[blockNum] = block.size();
                }
                // Set Alignment
                newAFPChain.setOptAln(newAlign);
                newAFPChain.setOptLen(blockLengths );
                newAFPChain.setOptLength(alignLen);
                newAFPChain.setBlockNum(blocks.size());
                newAFPChain.setBlockResSize(blockLengths.clone());
                newAFPChain.setSequentialAlignment(blocks.size() == 1);

                // TODO make the AFPSet consistent
                // TODO lots more block properties & old AFP properties

                // Recalculate superposition
                Atom[] atoms1 = new Atom[alignLen];
                Atom[] atoms2 = new Atom[alignLen];

                int pos=0;
                for(List<ResiduePair> block:blocks ) {
                        for(ResiduePair pair:block) {
                                atoms1[pos] = ca1[pair.a];
                                // Clone residue to allow modification
                                Atom atom2 = ca2duplicated[pair.b];
                                Group g = (Group) atom2.getGroup().clone();
                                atoms2[pos] = g.getAtom( atom2.getName() );
                                pos++;
                        }
                }
                assert(pos == alignLen);

                // Sets the rotation matrix in ceCalc to the proper value
                double rmsd = -1;
                double tmScore = 0.;
                double[] blockRMSDs = new double[blocks.size()];
                Matrix[] blockRotationMatrices = new Matrix[blocks.size()];
                Atom[] blockShifts = new Atom[blocks.size()];

                if(alignLen>0) {

                        // superimpose
                        Matrix4d trans = SuperPositions.superpose(Calc.atomsToPoints(atoms1),
                                        Calc.atomsToPoints(atoms2));

                        Matrix matrix = Matrices.getRotationJAMA(trans);
                        Atom shift = Calc.getTranslationVector(trans);

                        for( Atom a : atoms2 )
                                Calc.transform(a.getGroup(), trans);

                        //and get overall rmsd
                        rmsd = Calc.rmsd(atoms1, atoms2);
                        tmScore = Calc.getTMScore(atoms1, atoms2, ca1.length, ca2len);

                        // set all block rotations to the overall rotation
                        // It's not well documented if this is the expected behavior, but
                        // it seems to work.
                        blockRotationMatrices[0] = matrix;
                        blockShifts[0] = shift;
                        blockRMSDs[0] = -1;

                        for(int i=1;i<blocks.size();i++) {
                                blockRMSDs[i] = -1; //TODO Recalculate for the FATCAT text format
                                blockRotationMatrices[i] = (Matrix) blockRotationMatrices[0].clone();
                                blockShifts[i] = (Atom) blockShifts[0].clone();
                        }

                }
                newAFPChain.setOptRmsd(blockRMSDs);
                newAFPChain.setBlockRmsd(blockRMSDs);
                newAFPChain.setBlockRotationMatrix(blockRotationMatrices);
                newAFPChain.setBlockShiftVector(blockShifts);
                newAFPChain.setTotalRmsdOpt(rmsd);
                newAFPChain.setTMScore( tmScore );

                // Clean up remaining properties using the FatCat helper method
                Atom[] ca2 = new Atom[ca2len];
                System.arraycopy(ca2duplicated, 0, ca2, 0, ca2len);
                AFPAlignmentDisplay.getAlign(newAFPChain, ca1, ca2duplicated);

                return newAFPChain;
        }

        private static int[] countCtermResidues(int[] block, int blockLen,
                        int cEnd, int overlapLength) {
                int[] cTermResCount = new int[overlapLength+1]; // # res at or to the right of i within overlap
                cTermResCount[overlapLength] = 0;
                int alignPos = blockLen - 1;
                for(int i=overlapLength-1;i>=0;i--) { // i starts at the c-term and increases to the left
                        if(block[alignPos] == cEnd - overlapLength+1 + i) { // matches the aligned pair
                                // the c-term contains the -ith overlapping residue
                                cTermResCount[i] = cTermResCount[i+1]+1;
                                alignPos--;
                        } else {
                                cTermResCount[i] = cTermResCount[i+1];
                        }
                }
                return cTermResCount;
        }

        private static int[] countNtermResidues(int[] block, int nStart,
                        int overlapLength) {
                int[] nTermResCount = new int[overlapLength+1]; // increases monotonically
                nTermResCount[0] = 0;
                int alignPos = 0; // index of the next aligned pair

                for(int i=1;i<=overlapLength;i++) {
                        if(block[alignPos] == nStart + i-1 ) { // matches the aligned pair
                                // the n-term contains the ith overlapping residue
                                nTermResCount[i] = nTermResCount[i-1]+1;
                                alignPos++;
                        } else {
                                nTermResCount[i] = nTermResCount[i-1];
                        }
                }
                return nTermResCount;
        }


        /**
         * A light class to store an alignment between two residues.
         * @author Spencer Bliven
         * @see #filterDuplicateAFPs()
         */
        private static class ResiduePair {
                public int a;
                public int b;
                public ResiduePair(int a, int b) {
                        this.a=a;
                        this.b=b;
                }
                @Override
                public String toString() {
                        return a+":"+b;
                }
        }


        /**
         * Tiny wrapper for the disallowed regions of an alignment.
         * @see CeCPMain#calculateMinCP(int[], int, int, int)
         * @author Spencer Bliven
         *
         */
        protected static class CPRange {
                /**
                 * last allowed n-term
                 */
                public int n;
                /**
                 * midpoint of the alignment
                 */
                public int mid;
                /**
                 * first allowed c-term
                 */
                public int c;
        }

        /**
         * Finds the alignment index of the residues minCPlength before and after
         * the duplication.
         *
         * @param block The permuted block being considered, generally optAln[0][1]
         * @param blockLen The length of the block (in case extra memory was allocated in block)
         * @param ca2len The length, in residues, of the protein specified by block
         * @param minCPlength The minimum number of residues allowed for a CP
         * @return a CPRange with the following components:
         *  <dl><dt>n</dt><dd>Index into <code>block</code> of the residue such that
         *      <code>minCPlength</code> residues remain to the end of <code>ca2len</code>,
         *      or -1 if no residue fits that criterium.</dd>
         *  <dt>mid</dt><dd>Index of the first residue higher than <code>ca2len</code>.</dd>
         *  <dt>c</dt><dd>Index of <code>minCPlength</code>-th residue after ca2len,
         *      or ca2len*2 if no residue fits that criterium.</dd>
         *  </dl>
         */
        protected static CPRange calculateMinCP(int[] block, int blockLen, int ca2len, int minCPlength) {
                CPRange range = new CPRange();

                // Find the cut point within the alignment.
                // Either returns the index i of the alignment such that block[i] == ca2len,
                // or else returns -i-1 where block[i] is the first element > ca2len.
                int middle = Arrays.binarySearch(block, ca2len);
                if(middle < 0) {
                        middle = -middle -1;
                }
                // Middle is now the first res after the duplication
                range.mid = middle;

                int minCPntermIndex = middle-minCPlength;
                if(minCPntermIndex >= 0) {
                        range.n = block[minCPntermIndex];
                } else {
                        range.n = -1;
                }

                int minCPctermIndex = middle+minCPlength-1;
                if(minCPctermIndex < blockLen) {
                        range.c = block[minCPctermIndex];
                } else {
                        range.c = ca2len*2;
                }

                // Stub:
                // Best-case: assume all residues in the termini are aligned
                //range.n = ca2len - minCPlength;
                //range.c = ca2len + minCPlength-1;

                return range;
        }


        private static class CutPoint {
                public int numResiduesCut;
                public int firstRes;
                public int lastRes;
        }

        private static CutPoint calculateCutPoint(int[] block,int nStart, int cEnd,
                        int overlapLength, int alignLen, int minCPlength, int ca2len, int firstRes) {

                // We require at least minCPlength residues in a block.
                //TODO calculate these explicitely based on the alignment

                // The last valid n-term
                CPRange minCP = calculateMinCP(block, alignLen, ca2len, minCPlength);
                int minCPnterm = minCP.n;
                // The first valid c-term
                int minCPcterm = minCP.c;


                // # res at or to the left of i within the overlap
                int[] nTermResCount = countNtermResidues(block, nStart,
                                overlapLength);

                // Determine the position with the largest sum of lengths
                int[] cTermResCount = countCtermResidues(block, alignLen,
                                cEnd, overlapLength);

                // Alignment length for a cut at the left of the overlap
                int maxResCount=-1;
                for(int i=0;i<=overlapLength;i++) { // i is the position of the CP within the overlap region
                        // Calculate number of residues which remain after the CP
                        int nRemain,cRemain;
                        if(nStart+i <= minCPnterm) {
                                nRemain = nTermResCount[overlapLength]-nTermResCount[i];
                        } else {
                                nRemain = 0;
                        }
                        if(cEnd-overlapLength+i >= minCPcterm) {
                                cRemain = cTermResCount[0] - cTermResCount[i];
                        } else {
                                cRemain = 0;
                        }

                        // Look for the cut point which cuts off the minimum number of res
                        if(nRemain + cRemain > maxResCount ) { // '>' biases towards keeping the n-term
                                maxResCount = nRemain + cRemain;
                                firstRes = nStart+ i;
                        }
                }

                // Calculate the number of residues cut within the overlap
                int numResiduesCut = nTermResCount[overlapLength]+cTermResCount[0]-maxResCount;

                // Remove short blocks
                if(firstRes > minCPnterm) {
                        // update number of residues cut for those outside the overlap
                        numResiduesCut += 0; //TODO

                        firstRes = ca2len;
                }

                int lastRes = firstRes+ca2len-1;
                if(lastRes < minCPcterm) {
                        // update number of residues cut for those outside the overlap
                        numResiduesCut += 0; //TODO

                        lastRes = ca2len-1;
                }


                CutPoint cp = new CutPoint();
                cp.firstRes=firstRes;
                cp.numResiduesCut = numResiduesCut;
                cp.lastRes = lastRes;

                if(debug) {
                        System.out.format("Found a CP at residue %d. Trimming %d aligned residues from %d-%d of block 0 and %d-%d of block 1.\n",
                                        firstRes,cp.numResiduesCut,nStart,firstRes-1,firstRes, cEnd-ca2len);
                }

                return cp;
        }


        // try showing a GUI
        // requires additional dependencies biojava-structure-gui and JmolApplet
        // TODO dmyersturnbull: This should probably be in structure-gui
        @SuppressWarnings("unused")
        private static void displayAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws ClassNotFoundException, NoSuchMethodException, InvocationTargetException, IllegalAccessException, StructureException {
                Atom[] ca1clone = StructureTools.cloneAtomArray(ca1);
                Atom[] ca2clone = StructureTools.cloneAtomArray(ca2);
                if (! GuiWrapper.isGuiModuleInstalled()) {
                        System.err.println("The biojava-structure-gui and/or JmolApplet modules are not installed. Please install!");
                        // display alignment in console
                        System.out.println(afpChain.toCE(ca1clone, ca2clone));
                } else {
                        Object jmol = GuiWrapper.display(afpChain,ca1clone,ca2clone);
                        GuiWrapper.showAlignmentImage(afpChain, ca1clone,ca2clone,jmol);
                }
        }
}