public ThrowsTagImpl(String text, ClassDocImpl contextClass, MemberDocImpl contextMember) {
super(text);
char[] textarr = text.toCharArray();
int i = 0;
for (; i < textarr.length; ++i) {
if (!Parser.isWhitespace(textarr[i])) break;
}
for (; i < textarr.length; ++i) {
if (Parser.isWhitespace(textarr[i])) {
this.exceptionName = new String(textarr, 0, i).trim();
this.exceptionComment = new String(textarr, i, textarr.length - i).trim();
break;
}
}
if (null != exceptionName) {
if (contextClass == null) {
this.exception = Main.getRootDoc().classNamed(exceptionName);
} else {
this.exception = contextClass.findClass(exceptionName);
}
if (exception != null) this.exceptionName = exception.qualifiedName();
else {
if (text.trim().startsWith("<")) {
Main.getRootDoc()
.printWarning(
"Expected exception name but got '"
+ text
+ "' in class "
+ contextClass.getClassName());
}
}
} else {
Main.getRootDoc()
.printWarning(
"@throws tag in comment for "
+ contextClass.qualifiedName()
+ "."
+ contextMember.name()
+ " doesn't specify an exception.");
}
if (this.exceptionComment != null) {
setBody(this.exceptionComment, contextClass, contextMember);
}
}
public static void test1() {
Sequence[] seqs = Parser.test1();
double[][] distances = (new GappedHammingDistance()).getDistanceMatrix(seqs);
DecimalFormat f = new DecimalFormat("0000.000");
System.out.println(" " + seqs.length);
for (int i = 0; i < seqs.length; i++) {
System.out.print(seqs[i].name);
for (int k = 0; k < 10 - seqs[i].name.length(); k++) {
System.out.print(" ");
}
System.out.print(" ");
int cols = 1;
for (int j = 0; j < seqs.length; j++) {
if (i != j) {
int di = i;
int dj = j;
// force symmetric matrix - arg - what the???
// testing!!!
if (j > i) {
di = j;
dj = i;
}
double d = distances[di][dj];
// testing
if (d > 2000) {
System.err.println("ARGH");
}
System.out.print(f.format(d));
} else {
System.out.print(f.format(0));
}
System.out.print(" ");
cols++;
if (cols >= 7) {
System.out.println();
System.out.print(" ");
cols = 0;
}
}
if (cols != 7) {
System.out.println();
}
}
}
public static void run(
String infile,
String outfile,
String statsOutFile,
String distanceMeasureString,
String gapScalingFactorMultipliersString) {
// testing
// System.out.println ("zallstring that I heard in Driver.java: |" +
// gapScalingFactorMultipliersString + "|");
double[] gapScalingFactorMultipliers =
parseGapScalingFactorMultipliersString(gapScalingFactorMultipliersString);
Sequence[] seqs = Parser.parseMSA(infile);
// arg - to satisfy compiler
double[][] distances = new double[0][0];
DistanceWithGapMethod distance = getDistanceWithGapMethod(distanceMeasureString);
// unfortunately, for cache get/set - no easy way of outputting
// to stats file if logdet distance error occurred??
// so just output to STDOUT
if (distance instanceof GappedDistance) {
GappedDistance gappedDistance = (GappedDistance) distance;
// do this cache set only once per all GSFM settings
gappedDistance.cacheSetSimpleDistanceMatrices(seqs);
// rerun for all gsfm settings as necessary
for (int i = 0; i < gapScalingFactorMultipliers.length; i++) {
double gsfm = gapScalingFactorMultipliers[i];
// testing
// System.out.println (gsfm);
String gsfmOutfile = outfile + GSFM_FILENAME_DELIMITER + (new Double(gsfm)).toString();
String gsfmStatsOutfile =
statsOutFile + GSFM_FILENAME_DELIMITER + (new Double(gsfm)).toString();
// change printwriter to new filename
changePrintWriter(gsfmStatsOutfile);
distances = gappedDistance.cacheGetDistanceMatrix(gsfm);
Writer.writePhylipDistanceMatrix(seqs, distances, gsfmOutfile);
flushAndClosePrintWriter();
}
}
// LATER ADD IN PARAMETERIZING PASS IN MULTIPLE GAP OPEN/EXTEND
// PARAMETER COSTS FOR AFFINE DISTANCES
else if (distance instanceof AffineDistance) {
// parse out rest of parameters from distanceMeasureString
GapPenalties gapPenalties = parseAffineDistanceMeasureStringParameters(distanceMeasureString);
AffineDistance affineDistance = (AffineDistance) distance;
// do this cache set only once per all GSFM settings
affineDistance.cacheSetSimpleDistanceMatrices(seqs);
// rerun for all gsfm settings as necessary
// affine distance params
// concatenated onto affine distance name
for (int i = 0; i < gapScalingFactorMultipliers.length; i++) {
double gsfm = gapScalingFactorMultipliers[i];
String gsfmOutfile = outfile + GSFM_FILENAME_DELIMITER + (new Double(gsfm)).toString();
String gsfmStatsOutfile =
statsOutFile + GSFM_FILENAME_DELIMITER + (new Double(gsfm)).toString();
// WARNING - MUST MUST MUST have this set
// appropriately for both gsfm AND affine penalties!!!
// change printwriter to new filename
changePrintWriter(gsfmStatsOutfile);
distances =
affineDistance.cacheGetDistanceMatrix(
gsfm, gapPenalties.gapOpenPenalty, gapPenalties.gapExtendPenalty);
Writer.writePhylipDistanceMatrix(seqs, distances, gsfmOutfile);
flushAndClosePrintWriter();
}
} else { // no caching of simple distances for non-gapped distance methods
if ((gapScalingFactorMultipliers.length != 1) || (gapScalingFactorMultipliers[0] != 0.0)) {
printUsage();
System.exit(1);
}
String gsfmFilenameSuffix = GSFM_FILENAME_DELIMITER + gapScalingFactorMultipliers[0];
// change printwriter to filename
changePrintWriter(statsOutFile + gsfmFilenameSuffix);
distances = distance.getDistanceMatrix(seqs);
Writer.writePhylipDistanceMatrix(seqs, distances, outfile + gsfmFilenameSuffix);
flushAndClosePrintWriter();
}
}