/**
* Checks that the alignment given by afpChain is sequential. This means that the residue indices
* of both proteins increase monotonically as a function of the alignment position (ie both
* proteins are sorted).
*
* <p>This will return false for circularly permuted alignments or other non-topological
* alignments. It will also return false for cases where the alignment itself is sequential but it
* is not stored in the afpChain in a sorted manner.
*
* <p>Since algorithms which create non-sequential alignments split the alignment into multiple
* blocks, some computational time can be saved by only checking block boundaries for
* sequentiality. Setting <tt>checkWithinBlocks</tt> to <tt>true</tt> makes this function slower,
* but detects AFPChains with non-sequential blocks.
*
* <p>Note that this method should give the same results as {@link
* AFPChain#isSequentialAlignment()}. However, the AFPChain version relies on the
* StructureAlignment algorithm correctly setting this parameter, which is sadly not always the
* case.
*
* @param afpChain An alignment
* @param checkWithinBlocks Indicates whether individual blocks should be checked for
* sequentiality
* @return True if the alignment is sequential.
*/
public static boolean isSequentialAlignment(AFPChain afpChain, boolean checkWithinBlocks) {
int[][][] optAln = afpChain.getOptAln();
int[] alnLen = afpChain.getOptLen();
int blocks = afpChain.getBlockNum();
if (blocks < 1) return true; // trivial case
if (alnLen[0] < 1) return true;
// Check that blocks are sequential
if (checkWithinBlocks) {
for (int block = 0; block < blocks; block++) {
if (alnLen[block] < 1) continue; // skip empty blocks
int prevRes1 = optAln[block][0][0];
int prevRes2 = optAln[block][1][0];
for (int pos = 1; pos < alnLen[block]; pos++) {
int currRes1 = optAln[block][0][pos];
int currRes2 = optAln[block][1][pos];
if (currRes1 < prevRes1) {
return false;
}
if (currRes2 < prevRes2) {
return false;
}
prevRes1 = currRes1;
prevRes2 = currRes2;
}
}
}
// Check that blocks are sequential
int prevRes1 = optAln[0][0][alnLen[0] - 1];
int prevRes2 = optAln[0][1][alnLen[0] - 1];
for (int block = 1; block < blocks; block++) {
if (alnLen[block] < 1) continue; // skip empty blocks
if (optAln[block][0][0] < prevRes1) {
return false;
}
if (optAln[block][1][0] < prevRes2) {
return false;
}
prevRes1 = optAln[block][0][alnLen[block] - 1];
prevRes2 = optAln[block][1][alnLen[block] - 1];
}
return true;
}
/**
* Builds an {@link AFPChain} from already-matched arrays of atoms and residues.
*
* @param ca1 An array of atoms in the first structure
* @param ca2 An array of atoms in the second structure
* @param residues1 An array of {@link ResidueNumber ResidueNumbers} in the first structure that
* are aligned. Only null ResidueNumbers are considered to be unaligned
* @param residues2 An array of {@link ResidueNumber ResidueNumbers} in the second structure that
* are aligned. Only null ResidueNumbers are considered to be unaligned
* @throws StructureException
*/
private static AFPChain buildAlignment(
Atom[] ca1, Atom[] ca2, ResidueNumber[] residues1, ResidueNumber[] residues2)
throws StructureException {
// remove any gap
// this includes the ones introduced by the nullifying above
List<ResidueNumber> alignedResiduesList1 = new ArrayList<ResidueNumber>();
List<ResidueNumber> alignedResiduesList2 = new ArrayList<ResidueNumber>();
for (int i = 0; i < residues1.length; i++) {
if (residues1[i] != null && residues2[i] != null) {
alignedResiduesList1.add(residues1[i]);
alignedResiduesList2.add(residues2[i]);
}
}
ResidueNumber[] alignedResidues1 =
alignedResiduesList1.toArray(new ResidueNumber[alignedResiduesList1.size()]);
ResidueNumber[] alignedResidues2 =
alignedResiduesList2.toArray(new ResidueNumber[alignedResiduesList2.size()]);
AFPChain afpChain = AlignmentTools.createAFPChain(ca1, ca2, alignedResidues1, alignedResidues2);
afpChain.setAlgorithmName("unknown");
AlignmentTools.updateSuperposition(afpChain, ca1, ca2);
afpChain.setBlockSize(new int[] {afpChain.getNrEQR()});
afpChain.setBlockRmsd(new double[] {afpChain.getTotalRmsdOpt()});
afpChain.setBlockGap(new int[] {afpChain.getGapLen()});
return afpChain;
}
/**
* Creates a Map specifying the alignment as a mapping between residue indices of protein 1 and
* residue indices of protein 2.
*
* <p>For example,
*
* <pre>
* 1234
* 5678</pre>
*
* becomes
*
* <pre>
* 1->5
* 2->6
* 3->7
* 4->8</pre>
*
* @param afpChain An alignment
* @return A mapping from aligned residues of protein 1 to their partners in protein 2.
* @throws StructureException If afpChain is not one-to-one
*/
public static Map<Integer, Integer> alignmentAsMap(AFPChain afpChain) throws StructureException {
Map<Integer, Integer> map = new HashMap<Integer, Integer>();
if (afpChain.getAlnLength() < 1) {
return map;
}
int[][][] optAln = afpChain.getOptAln();
int[] optLen = afpChain.getOptLen();
for (int block = 0; block < afpChain.getBlockNum(); block++) {
for (int pos = 0; pos < optLen[block]; pos++) {
int res1 = optAln[block][0][pos];
int res2 = optAln[block][1][pos];
if (map.containsKey(res1)) {
throw new StructureException(
String.format("Residue %d aligned to both %d and %d.", res1, map.get(res1), res2));
}
map.put(res1, res2);
}
}
return map;
}
/**
* Retrieves the optimum alignment from an AFPChain and returns it as a java collection. The
* result is indexed in the same way as {@link AFPChain#getOptAln()}, but has the correct size().
*
* <pre>
* List<List<List<Integer>>> aln = getOptAlnAsList(AFPChain afpChain);
* aln.get(blockNum).get(structureNum={0,1}).get(pos)</pre>
*
* @param afpChain
* @return
*/
public static List<List<List<Integer>>> getOptAlnAsList(AFPChain afpChain) {
int[][][] optAln = afpChain.getOptAln();
int[] optLen = afpChain.getOptLen();
List<List<List<Integer>>> blocks = new ArrayList<List<List<Integer>>>(afpChain.getBlockNum());
for (int blockNum = 0; blockNum < afpChain.getBlockNum(); blockNum++) {
// TODO could improve speed an memory by wrapping the arrays with
// an unmodifiable list, similar to Arrays.asList(...) but with the
// correct size parameter.
List<Integer> align1 = new ArrayList<Integer>(optLen[blockNum]);
List<Integer> align2 = new ArrayList<Integer>(optLen[blockNum]);
for (int pos = 0; pos < optLen[blockNum]; pos++) {
align1.add(optAln[blockNum][0][pos]);
align2.add(optAln[blockNum][1][pos]);
}
List<List<Integer>> block = new ArrayList<List<Integer>>(2);
block.add(align1);
block.add(align2);
blocks.add(block);
}
return blocks;
}
/**
* Conditions checked are: score above the threshold, order higher than 1 and refinement
* succeeded.
*
* @return true if significant, false otherwise
*/
public boolean isSignificant() {
// In any case if the order is 1 it is asymmetric
if (symmOrder < 2) return false;
// If the TM-Score is below the threshold
if (selfAlignment.getTMScore() < params.getScoreThreshold()) return false;
// If the refinement was attempted
if (params.getRefineMethod() != RefineMethod.NOT_REFINED) {
// Check for minimum length
if (multipleAlignment.getCoreLength() < params.getMinCoreLength()) return false;
// Allow 90% of original TM-Score theshold
if (multipleAlignment.getScore(MultipleAlignmentScorer.AVGTM_SCORE)
< params.getScoreThreshold() * 0.9) return false;
return true;
}
return true;
}
/**
* @param afpChain Input afpchain. UNMODIFIED
* @param ca1
* @param ca2
* @param optLens
* @param optAln
* @return A NEW AfpChain based off the input but with the optAln modified
* @throws StructureException if an error occured during superposition
*/
public static AFPChain replaceOptAln(
AFPChain afpChain, Atom[] ca1, Atom[] ca2, int blockNum, int[] optLens, int[][][] optAln)
throws StructureException {
int optLength = 0;
for (int blk = 0; blk < blockNum; blk++) {
optLength += optLens[blk];
}
// set everything
AFPChain refinedAFP = (AFPChain) afpChain.clone();
refinedAFP.setOptLength(optLength);
refinedAFP.setBlockSize(optLens);
refinedAFP.setOptLen(optLens);
refinedAFP.setOptAln(optAln);
refinedAFP.setBlockNum(blockNum);
// TODO recalculate properties: superposition, tm-score, etc
Atom[] ca2clone = StructureTools.cloneAtomArray(ca2); // don't modify ca2 positions
AlignmentTools.updateSuperposition(refinedAFP, ca1, ca2clone);
AFPAlignmentDisplay.getAlign(refinedAFP, ca1, ca2clone);
return refinedAFP;
}
/**
* After the alignment changes (optAln, optLen, blockNum, at a minimum), many other properties
* which depend on the superposition will be invalid.
*
* <p>This method re-runs a rigid superposition over the whole alignment and repopulates the
* required properties, including RMSD (TotalRMSD) and TM-Score.
*
* @param afpChain
* @param ca1
* @param ca2 Second set of ca atoms. Will be modified based on the superposition
* @throws StructureException
* @see {@link CECalculator#calc_rmsd(Atom[], Atom[], int, boolean)} contains much of the same
* code, but stores results in a CECalculator instance rather than an AFPChain
*/
public static void updateSuperposition(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
throws StructureException {
// Update ca information, because the atom array might also be changed
afpChain.setCa1Length(ca1.length);
afpChain.setCa2Length(ca2.length);
// We need this to get the correct superposition
int[] focusRes1 = afpChain.getFocusRes1();
int[] focusRes2 = afpChain.getFocusRes2();
if (focusRes1 == null) {
focusRes1 = new int[afpChain.getCa1Length()];
afpChain.setFocusRes1(focusRes1);
}
if (focusRes2 == null) {
focusRes2 = new int[afpChain.getCa2Length()];
afpChain.setFocusRes2(focusRes2);
}
if (afpChain.getNrEQR() == 0) return;
// create new arrays for the subset of atoms in the alignment.
Atom[] ca1aligned = new Atom[afpChain.getOptLength()];
Atom[] ca2aligned = new Atom[afpChain.getOptLength()];
int pos = 0;
int[] blockLens = afpChain.getOptLen();
int[][][] optAln = afpChain.getOptAln();
assert (afpChain.getBlockNum() <= optAln.length);
for (int block = 0; block < afpChain.getBlockNum(); block++) {
for (int i = 0; i < blockLens[block]; i++) {
int pos1 = optAln[block][0][i];
int pos2 = optAln[block][1][i];
Atom a1 = ca1[pos1];
Atom a2 = (Atom) ca2[pos2].clone();
ca1aligned[pos] = a1;
ca2aligned[pos] = a2;
pos++;
}
}
// this can happen when we load an old XML serialization which did not support modern ChemComp
// representation of modified residues.
if (pos != afpChain.getOptLength()) {
logger.warn(
"AFPChainScorer getTMScore: Problems reconstructing alignment! nr of loaded atoms is "
+ pos
+ " but should be "
+ afpChain.getOptLength());
// we need to resize the array, because we allocated too many atoms earlier on.
ca1aligned = (Atom[]) resizeArray(ca1aligned, pos);
ca2aligned = (Atom[]) resizeArray(ca2aligned, pos);
}
// Superimpose the two structures in correspondance to the new alignment
SVDSuperimposer svd = new SVDSuperimposer(ca1aligned, ca2aligned);
Matrix matrix = svd.getRotation();
Atom shift = svd.getTranslation();
Matrix[] blockMxs = new Matrix[afpChain.getBlockNum()];
Arrays.fill(blockMxs, matrix);
afpChain.setBlockRotationMatrix(blockMxs);
Atom[] blockShifts = new Atom[afpChain.getBlockNum()];
Arrays.fill(blockShifts, shift);
afpChain.setBlockShiftVector(blockShifts);
for (Atom a : ca2aligned) {
Calc.rotate(a, matrix);
Calc.shift(a, shift);
}
// Calculate the RMSD and TM score for the new alignment
double rmsd = SVDSuperimposer.getRMS(ca1aligned, ca2aligned);
double tmScore = SVDSuperimposer.getTMScore(ca1aligned, ca2aligned, ca1.length, ca2.length);
afpChain.setTotalRmsdOpt(rmsd);
afpChain.setTMScore(tmScore);
// Calculate the RMSD and TM score for every block of the new alignment
double[] blockRMSD = new double[afpChain.getBlockNum()];
double[] blockScore = new double[afpChain.getBlockNum()];
for (int k = 0; k < afpChain.getBlockNum(); k++) {
// Create the atom arrays corresponding to the aligned residues in the block
Atom[] ca1block = new Atom[afpChain.getOptLen()[k]];
Atom[] ca2block = new Atom[afpChain.getOptLen()[k]];
int position = 0;
for (int i = 0; i < blockLens[k]; i++) {
int pos1 = optAln[k][0][i];
int pos2 = optAln[k][1][i];
Atom a1 = ca1[pos1];
Atom a2 = (Atom) ca2[pos2].clone();
ca1block[position] = a1;
ca2block[position] = a2;
position++;
}
if (position != afpChain.getOptLen()[k]) {
logger.warn(
"AFPChainScorer getTMScore: Problems reconstructing block alignment! nr of loaded atoms is "
+ pos
+ " but should be "
+ afpChain.getOptLen()[k]);
// we need to resize the array, because we allocated too many atoms earlier on.
ca1block = (Atom[]) resizeArray(ca1block, position);
ca2block = (Atom[]) resizeArray(ca2block, position);
}
// Superimpose the two block structures
SVDSuperimposer svdb = new SVDSuperimposer(ca1block, ca2block);
Matrix matrixb = svdb.getRotation();
Atom shiftb = svdb.getTranslation();
for (Atom a : ca2block) {
Calc.rotate(a, matrixb);
Calc.shift(a, shiftb);
}
// Calculate the RMSD and TM score for the block
double rmsdb = SVDSuperimposer.getRMS(ca1block, ca2block);
double tmScoreb = SVDSuperimposer.getTMScore(ca1block, ca2block, ca1.length, ca2.length);
blockRMSD[k] = rmsdb;
blockScore[k] = tmScoreb;
}
afpChain.setOptRmsd(blockRMSD);
afpChain.setBlockRmsd(blockRMSD);
afpChain.setBlockScore(blockScore);
}
/**
* It replaces an optimal alignment of an AFPChain and calculates all the new alignment scores and
* variables.
*/
public static AFPChain replaceOptAln(int[][][] newAlgn, AFPChain afpChain, Atom[] ca1, Atom[] ca2)
throws StructureException {
// The order is the number of groups in the newAlgn
int order = newAlgn.length;
// Calculate the alignment length from all the subunits lengths
int[] optLens = new int[order];
for (int s = 0; s < order; s++) {
optLens[s] = newAlgn[s][0].length;
}
int optLength = 0;
for (int s = 0; s < order; s++) {
optLength += optLens[s];
}
// Create a copy of the original AFPChain and set everything needed for the structure update
AFPChain copyAFP = (AFPChain) afpChain.clone();
// Set the new parameters of the optimal alignment
copyAFP.setOptLength(optLength);
copyAFP.setOptLen(optLens);
copyAFP.setOptAln(newAlgn);
// Set the block information of the new alignment
copyAFP.setBlockNum(order);
copyAFP.setBlockSize(optLens);
copyAFP.setBlockResList(newAlgn);
copyAFP.setBlockResSize(optLens);
copyAFP.setBlockGap(calculateBlockGap(newAlgn));
// Recalculate properties: superposition, tm-score, etc
Atom[] ca2clone = StructureTools.cloneAtomArray(ca2); // don't modify ca2 positions
AlignmentTools.updateSuperposition(copyAFP, ca1, ca2clone);
// It re-does the sequence alignment strings from the OptAlgn information only
copyAFP.setAlnsymb(null);
AFPAlignmentDisplay.getAlign(copyAFP, ca1, ca2clone);
return copyAFP;
}
/**
* @param a
* @param ca1
* @param ca2
* @return
* @throws StructureException if an error occurred during superposition
*/
public static AFPChain splitBlocksByTopology(AFPChain a, Atom[] ca1, Atom[] ca2)
throws StructureException {
int[][][] optAln = a.getOptAln();
int blockNum = a.getBlockNum();
int[] optLen = a.getOptLen();
// Determine block lengths
// Split blocks if residue indices don't increase monotonically
List<Integer> newBlkLen = new ArrayList<Integer>();
boolean blockChanged = false;
for (int blk = 0; blk < blockNum; blk++) {
int currLen = 1;
for (int pos = 1; pos < optLen[blk]; pos++) {
if (optAln[blk][0][pos] <= optAln[blk][0][pos - 1]
|| optAln[blk][1][pos] <= optAln[blk][1][pos - 1]) {
// start a new block
newBlkLen.add(currLen);
currLen = 0;
blockChanged = true;
}
currLen++;
}
if (optLen[blk] < 2) {
newBlkLen.add(optLen[blk]);
} else {
newBlkLen.add(currLen);
}
}
// Check if anything needs to be split
if (!blockChanged) {
return a;
}
// Split blocks
List<int[][]> blocks = new ArrayList<int[][]>(newBlkLen.size());
int oldBlk = 0;
int pos = 0;
for (int blkLen : newBlkLen) {
if (blkLen == optLen[oldBlk]) {
assert (pos == 0); // should be the whole block
// Use the old block
blocks.add(optAln[oldBlk]);
} else {
int[][] newBlock = new int[2][blkLen];
assert (pos + blkLen <= optLen[oldBlk]); // don't overrun block
for (int i = 0; i < blkLen; i++) {
newBlock[0][i] = optAln[oldBlk][0][pos + i];
newBlock[1][i] = optAln[oldBlk][1][pos + i];
}
pos += blkLen;
blocks.add(newBlock);
if (pos == optLen[oldBlk]) {
// Finished this oldBlk, start the next
oldBlk++;
pos = 0;
}
}
}
// Store new blocks
int[][][] newOptAln = blocks.toArray(new int[0][][]);
int[] newBlockLens = new int[newBlkLen.size()];
for (int i = 0; i < newBlkLen.size(); i++) {
newBlockLens[i] = newBlkLen.get(i);
}
return replaceOptAln(a, ca1, ca2, blocks.size(), newBlockLens, newOptAln);
}
/**
* Fundamentally, an alignment is just a list of aligned residues in each protein. This method
* converts two lists of ResidueNumbers into an AFPChain.
*
* <p>Parameters are filled with defaults (often null) or sometimes calculated.
*
* <p>For a way to modify the alignment of an existing AFPChain, see {@link
* AlignmentTools#replaceOptAln(AFPChain, Atom[], Atom[], Map)}
*
* @param ca1 CA atoms of the first protein
* @param ca2 CA atoms of the second protein
* @param aligned1 A list of aligned residues from the first protein
* @param aligned2 A list of aligned residues from the second protein. Must be the same length as
* aligned1.
* @return An AFPChain representing the alignment. Many properties may be null or another default.
* @throws StructureException if an error occured during superposition
* @throws IllegalArgumentException if aligned1 and aligned2 have different lengths
* @see AlignmentTools#replaceOptAln(AFPChain, Atom[], Atom[], Map)
*/
public static AFPChain createAFPChain(
Atom[] ca1, Atom[] ca2, ResidueNumber[] aligned1, ResidueNumber[] aligned2)
throws StructureException {
// input validation
int alnLen = aligned1.length;
if (alnLen != aligned2.length) {
throw new IllegalArgumentException("Alignment lengths are not equal");
}
AFPChain a = new AFPChain(AFPChain.UNKNOWN_ALGORITHM);
try {
a.setName1(ca1[0].getGroup().getChain().getStructure().getName());
if (ca2[0].getGroup().getChain().getStructure() != null) {
// common case for cloned ca2
a.setName2(ca2[0].getGroup().getChain().getStructure().getName());
}
} catch (Exception e) {
// One of the structures wasn't fully created. Ignore
}
a.setBlockNum(1);
a.setCa1Length(ca1.length);
a.setCa2Length(ca2.length);
a.setOptLength(alnLen);
a.setOptLen(new int[] {alnLen});
Matrix[] ms = new Matrix[a.getBlockNum()];
a.setBlockRotationMatrix(ms);
Atom[] blockShiftVector = new Atom[a.getBlockNum()];
a.setBlockShiftVector(blockShiftVector);
String[][][] pdbAln = new String[1][2][alnLen];
for (int i = 0; i < alnLen; i++) {
pdbAln[0][0][i] = aligned1[i].getChainId() + ":" + aligned1[i];
pdbAln[0][1][i] = aligned2[i].getChainId() + ":" + aligned2[i];
}
a.setPdbAln(pdbAln);
// convert pdbAln to optAln, and fill in some other basic parameters
AFPChainXMLParser.rebuildAFPChain(a, ca1, ca2);
return a;
// Currently a single block. Split into several blocks by sequence if needed
// return AlignmentTools.splitBlocksByTopology(a,ca1,ca2);
}
/**
* Creates a simple interaction format (SIF) file for an alignment.
*
* <p>The SIF file can be read by network software (eg Cytoscape) to analyze alignments as graphs.
*
* <p>This function creates a graph with residues as nodes and two types of edges: 1. backbone
* edges, which connect adjacent residues in the aligned protein 2. alignment edges, which connect
* aligned residues
*
* @param out Stream to write to
* @param afpChain alignment to write
* @param ca1 First protein, used to generate node names
* @param ca2 Second protein, used to generate node names
* @param backboneInteraction Two-letter string used to identify backbone edges
* @param alignmentInteraction Two-letter string used to identify alignment edges
* @throws IOException
*/
public static void alignmentToSIF(
Writer out,
AFPChain afpChain,
Atom[] ca1,
Atom[] ca2,
String backboneInteraction,
String alignmentInteraction)
throws IOException {
// out.write("Res1\tInteraction\tRes2\n");
String name1 = afpChain.getName1();
String name2 = afpChain.getName2();
if (name1 == null) name1 = "";
else name1 += ":";
if (name2 == null) name2 = "";
else name2 += ":";
// Print alignment edges
int nblocks = afpChain.getBlockNum();
int[] blockLen = afpChain.getOptLen();
int[][][] optAlign = afpChain.getOptAln();
for (int b = 0; b < nblocks; b++) {
for (int r = 0; r < blockLen[b]; r++) {
int res1 = optAlign[b][0][r];
int res2 = optAlign[b][1][r];
ResidueNumber rn1 = ca1[res1].getGroup().getResidueNumber();
ResidueNumber rn2 = ca2[res2].getGroup().getResidueNumber();
String node1 = name1 + rn1.getChainId() + rn1.toString();
String node2 = name2 + rn2.getChainId() + rn2.toString();
out.write(String.format("%s\t%s\t%s\n", node1, alignmentInteraction, node2));
}
}
// Print first backbone edges
ResidueNumber rn = ca1[0].getGroup().getResidueNumber();
String last = name1 + rn.getChainId() + rn.toString();
for (int i = 1; i < ca1.length; i++) {
rn = ca1[i].getGroup().getResidueNumber();
String curr = name1 + rn.getChainId() + rn.toString();
out.write(String.format("%s\t%s\t%s\n", last, backboneInteraction, curr));
last = curr;
}
// Print second backbone edges, if the proteins differ
// Do some quick checks for whether the proteins differ
// (Not perfect, but should detect major differences and CPs.)
if (!name1.equals(name2)
|| ca1.length != ca2.length
|| (ca1.length > 0
&& ca1[0].getGroup() != null
&& ca2[0].getGroup() != null
&& !ca1[0]
.getGroup()
.getResidueNumber()
.equals(ca2[0].getGroup().getResidueNumber()))) {
rn = ca2[0].getGroup().getResidueNumber();
last = name2 + rn.getChainId() + rn.toString();
for (int i = 1; i < ca2.length; i++) {
rn = ca2[i].getGroup().getResidueNumber();
String curr = name2 + rn.getChainId() + rn.toString();
out.write(String.format("%s\t%s\t%s\n", last, backboneInteraction, curr));
last = curr;
}
}
}
public void testOldSecOutput() throws Exception {
String fileName = "/ce_1fdo.A_2iv2.X.out";
InputStream inStream = this.getClass().getResourceAsStream(fileName);
assertNotNull("Could not find file " + fileName + " in resource path. Config error?", inStream);
String xml = StringManipulationHelper.convertStreamToString(inStream);
AtomCache cache = new AtomCache();
String name1 = "1FDO.A";
String name2 = "2IV2.X";
Atom[] ca1 = cache.getAtoms(name1);
Atom[] ca2 = cache.getAtoms(name2);
assertEquals(715, ca1.length);
assertEquals(697, ca2.length);
AFPChain afpChainOrig = AFPChainXMLParser.fromXML(xml, ca1, ca2);
assertNotNull("Could not get AfpChain object from flat file!", afpChainOrig);
assertEquals(
"Could not find alignment string for prot 1",
"MKKVVTVCPYCASGCKINLVVDNGKIVRAEAAQGKTNQGTLCLKGYYGWDFINDTQILTPRLKTPMIRRQRGGKLEPVSWDEALNYVAERLSAIKEKYGPDAIQTTGSSRGTGNETNYVMQKFARAVIGTNNVDCCARVUHGPSVA-----GLHQSVGNGAMSNAINEIDNTDLVFVFGYNPADSHPIVANHVINAKRNGAKIIVCDPRKIETARIADMHIALKNGSNIALLNAMGHVIIEENLYDKAFVASRTEGFEEYRKIVEGYTPESVEDITGVSASEIRQAARMYAQAKSAAILWGMGVTQFYQGVETVRSLTSLAMLTGNLGKPHAGVNPVRGQNNVQGACDMGALPDTYPGYQYVKDPANREKFAKAWGVESLPAHTGYRISELPHRAAHGEVRAAYIMGEDPLQTDAELSAVRKAFEDLELVIVQDIFMTKTASAADVILPSTSWGEHEGVFTAADRGFQRFFKAVEPKWDLKTDWQIISEIATRMGYPMHYNNTQEIWDELRHLCPDFYGATYEKMGELGFIQWPCRDTSDADQGTSYLFKEKFDTPNGLAQFFTCDWVAPIDKLTDEYPMVLSTVREVGHYSCRSMTGNCAALAALADEPGYAQINTEDAKRLGIEDEALVWVHSRKGKIITRAQVSDRPNKGAIYMTYQWWIGACNELVTENLSPITKTPEYKYCAVRVEPIADQRAAEQYVIDEYNKLKTRLREAALA",
new String(afpChainOrig.getAlnseq1(), 0, afpChainOrig.getAlnLength()));
assertEquals(
"Could not find alignment string for prot 2",
"MKKVVTVCPYCASGCKINLVVDNGKIVRAEAAQGKTNQGTLCLKGYYGWDFINDTQILTPRLKTPMIRRQRGGKLEPVSWDEALNYVAERLSAIKEKYGPDAIQTTGSSRGTGNETNYVMQKFARAVIGTNNVDCCAR-----VUHGPSVAGLHQSVGNGAMSNAINEIDNTDLVFVFGYNPADSHPIVANHVINAKRNGAKIIVCDPRKIETARIADMHIALKNGSNIALLNAMGHVIIEENLYDKAFVASRTEGFEEYRKIVEGYTPESVEDITGVSASEIRQAARMYAQAKSAAILWGMGVTQFYQGVETVRSLTSLAMLTGNLGKPHAGVNPVRGQNNVQGACDMGALPDTYPGYQYVKDPANREKFAKAWGVESLPAHTGYRISELPHRAAHGEVRAAYIMGEDPLQTDAELSAVRKAFEDLELVIVQDIFMTKTASAADVILPSTSWGEHEGVFTAADRGFQRFFKAVEPKWDLKTDWQIISEIATRMGYPMHYNNTQEIWDELRHLCPDFYGATYEKMGELGFIQWPCRDTSDADQGTSYLFKEKFDTPNGLAQFFTCDWVAPIDKLTDEYPMVLSTVREVGHYSCRSMTGNCAALAALADEPGYAQINTEDAKRLGIEDEALVWVHSRKGKIITRAQVSDRPNKGAIYMTYQWW------------------PEYKYCAVRVEPIADQRAAEQYVIDEYNKLKTRLREAALA",
new String(afpChainOrig.getAlnseq2(), 0, afpChainOrig.getAlnLength()));
// calc time is hardware dependent.... overwrite...
afpChainOrig.setCalculationTime(-1);
assertEquals(
"alnLength is wrong! (" + afpChainOrig.getAfpChainLen() + ")",
720,
afpChainOrig.getAlnLength());
assertEquals(
"gapLength is wrong! (" + afpChainOrig.getGapLen() + ")", 28, afpChainOrig.getGapLen());
// identity should be 0.9569
assertTrue(
"alinment ID is < 0.95 ! (" + afpChainOrig.getIdentity() + ")",
afpChainOrig.getIdentity() > 0.95);
assertTrue(
"alignment ID is > 0.96 ! (" + afpChainOrig.getIdentity() + ")",
afpChainOrig.getIdentity() < 0.96);
String xmlComp = AFPChainXMLConverter.toXML(afpChainOrig, ca1, ca2);
FlipAFPChainTest t = new FlipAFPChainTest();
t.printFirstMismatch(xml, xmlComp);
StringManipulationTestsHelper.assertEqualsIgnoreEndline(xml, xmlComp);
StructureAlignment ce = StructureAlignmentFactory.getAlgorithm(CeMain.algorithmName);
AFPChain afpChainNew = ce.align(ca1, ca2);
afpChainNew.setCalculationTime(-1);
afpChainNew.setName1(name1);
afpChainNew.setName2(name2);
String xmlNew = AFPChainXMLConverter.toXML(afpChainNew, ca1, ca2);
StringManipulationTestsHelper.assertEqualsIgnoreEndline(xml, xmlNew);
}