Performs alignment
176821
protected void align() {
		if (!isReady()) {
			return;
		}

		long timeStart = System.nanoTime();

		int[] dim = getScoreMatrixDimensions();
		if (storingScoreMatrix) {
			scores = new int[dim[0]][dim[1]][dim[2]];
		} else {
			scores = new int[dim[0]][][];
			scores[0] = new int[dim[1]][dim[2]];
			scores[1] = new int[dim[1]][dim[2]];
		}
		boolean linear = (gapPenalty.getType() == GapPenalty.Type.LINEAR);
		Last[][][] traceback = new Last[dim[0]][][];
		List<Step> sx = new ArrayList<Step>(), sy = new ArrayList<Step>();

		if (!local) {
			xyMax = new int[] { dim[0] - 1, dim[1] - 1 };
			xyStart = new int[] { 0, 0 };
			score = 0;
			List<Subproblem> problems = Subproblem.getSubproblems(anchors, xyMax[0], xyMax[1]);
			assert problems.size() == anchors.size() + 1;
			for (int i = 0; i < problems.size(); i++) {
				Subproblem subproblem = problems.get(i);
				for (int x = subproblem.getQueryStartIndex(); x <= subproblem.getQueryEndIndex(); x++) {

					traceback[x] =

					  linear ?
						setScoreVector(x, subproblem, gapPenalty.getExtensionPenalty(), getSubstitutionScoreVector(x, subproblem), storingScoreMatrix, scores) :

						setScoreVector(x, subproblem, gapPenalty.getOpenPenalty(), gapPenalty.getExtensionPenalty(), getSubstitutionScoreVector(x, subproblem), storingScoreMatrix, scores);
				}
			}
			setSteps(traceback, scores, sx, sy);
			score = Integer.MIN_VALUE;
			int[] finalScore = scores[xyMax[0]][xyMax[1]];
			for (int z = 0; z < finalScore.length; z++) {
				score = Math.max(score, finalScore[z]);
			}
		} else {
			for (int x = 0; x < dim[0]; x++) {

				traceback[x] =

				  linear ?
					setScoreVector(x, gapPenalty.getExtensionPenalty(), getSubstitutionScoreVector(x), storingScoreMatrix, scores, xyMax, score) :

					setScoreVector(x, gapPenalty.getOpenPenalty(), gapPenalty.getExtensionPenalty(), getSubstitutionScoreVector(x), storingScoreMatrix, scores, xyMax, score);

				if (xyMax[0] == x) {
					score = scores[x][xyMax[1]][0];
				}
			}
			xyStart = local ? setSteps(traceback, xyMax, sx, sy) : setSteps(traceback, scores, sx, sy);
		}

		setProfile(sx, sy);

		if (!storingScoreMatrix) {
			scores = null;
		}

		time = System.nanoTime() - timeStart;
	}
931666
def alignment_a(self):
        
        from molmod.transformations import Rotation
        new_x = self.matrix[:, 0].copy()
        new_x /= np.linalg.norm(new_x)
        new_z = np.cross(new_x, self.matrix[:, 1])
        new_z /= np.linalg.norm(new_z)
        new_y = np.cross(new_z, new_x)
        new_y /= np.linalg.norm(new_y)
        return Rotation(np.array([new_x, new_y, new_z]))
600183
def organize_noalign(data):
    
    data = utils.to_single_data(data[0])
    work_dir = utils.safe_makedir(os.path.join(dd.get_work_dir(data), "align", dd.get_sample_name(data)))
    work_bam = os.path.join(work_dir, "%s-input.bam" % dd.get_sample_name(data))
    if data.get("files"):
        if data["files"][0].endswith(".cram"):
            work_bam = cram.to_bam(data["files"][0], work_bam, data)
        else:
            assert data["files"][0].endswith(".bam"), data["files"][0]
            utils.copy_plus(data["files"][0], work_bam)
        bam.index(work_bam, data["config"])
    else:
        work_bam = None
    data["align_bam"] = work_bam
    return data
1041256
public void setAlignment(int alignment) {
        super.setAlignment(alignment);
        for(int i = 0; i < this.content.length; i++) {
            if(this.content[i] instanceof Paragraph) {
                ((Paragraph) this.content[i]).setAlignment(alignment);
            } else if(this.content[i] instanceof Table) {
                ((Table) this.content[i]).setAlignment(alignment);
            } else if(this.content[i] instanceof Image) {
                ((Image) this.content[i]).setAlignment(alignment);
            }     
        }
    }
408426
def template_align(self, ref_path):
        """"""
        # Run it #
        sh.mothur("#align.seqs(candidate=%s, template=%s, search=blast, flip=false, processors=8);" % (self.path, ref_path))
        # Move things #
        shutil.move(self.path[:-6] + '.align',        self.p.aligned)
        shutil.move(self.path[:-6] + '.align.report', self.p.report)
        shutil.move(self.path[:-6] + '.flip.accnos',  self.p.accnos)
        # Clean up #
        if os.path.exists('formatdb.log'): os.remove('formatdb.log')
        if os.path.exists('error.log') and os.path.getsize('error.log') == 0: os.remove('error.log')
        for p in sh.glob('mothur.*.logfile'): os.remove(p)
898540
def align(s1, s2, gap=' ', eq=operator.eq):
    '''

    '''
    # first we compute the dynamic programming table
    m, n = len(s1), len(s2)
    table = []  # the table is extended lazily, one row at a time
    row = list(range(n+1))  # the first row is 0, 1, 2, ..., n
    table.append(list(row))  # copy row and insert into table
    for i in range(m):
        p = i
        row[0] = i+1
        for j in range(n):
            t = 0 if eq(s1[i], s2[j]) else 1
            p, row[j+1] = row[j+1], min(p+t, row[j]+1, row[j+1]+1)
        table.append(list(row))  # copy row and insert into table
    # now we trace the best alignment path from cell [m][n] to cell [0],[0]
    s1_, s2_ = '', ''

    i, j = m, n
    while i != 0 and j != 0:
        _, i, j, s1_, s2_ = min(
            (table[i-1][j-1], i-1, j-1, s1[i-1]+s1_, s2[j-1]+s2_),
            (table[i-1][j], i-1, j, s1[i-1]+s1_, gap+s2_),
            (table[i][j-1], i, j-1, gap+s1_, s2[j-1]+s2_)
        )
    if i != 0:
        s1_ = s1[:i]+s1_
        s2_ = gap*i+s2_
    if j != 0:
        s1_ = gap*j+s1_
        s2_ = s2[:j]+s2_
    return s1_, s2_
225950
def align_after(self, offset):
        
        f = self.reader
        if offset <= 0:  # FIXME what is a negative offset??
            f.seek(0)
            self._block_count = 0
            self._read_header()  # FIXME we can't extimate how big it is...
            return
        sm = self.sync_marker
        sml = len(sm)
        pos = offset
        while pos < self.file_length - sml:
            f.seek(pos)
            data = f.read(self.FORWARD_WINDOW_SIZE)
            sync_offset = data.find(sm)
            if sync_offset > -1:
                f.seek(pos + sync_offset)
                self._block_count = 0
                return
            pos += len(data)
625237
public void align(Object... s) {
    if (alignedBlock == null) {
      alignedBlock = new AlignedBlock(this);
    }
    alignedBlock.align(s);
  }
373146
def add_alignment(self,align):
    """"""
    self._target_context_errors = None
    self._query_context_errors = None
    ae = AlignmentErrors(align)
    self._alignment_errors.append(ae)
    self._general_errors.add_alignment_errors(ae)
1284814
def _align_column(strings, alignment, minwidth=0,
                  has_invisible=True, enable_widechars=False, is_multiline=False):
    """"""
    strings, padfn = _align_column_choose_padfn(
        strings, alignment, has_invisible)
    width_fn = _choose_width_fn(has_invisible, enable_widechars, is_multiline)

    s_widths = list(map(width_fn, strings))
    maxwidth = max(max(s_widths), minwidth)
    # TODO: refactor column alignment in single-line and multiline modes
    if is_multiline:
        if not enable_widechars and not has_invisible:
            padded_strings = [
                "\n".join([padfn(maxwidth, s) for s in ms.splitlines()])
                for ms in strings]
        else:
            # enable wide-character width corrections
            s_lens = [max((len(s) for s in re.split("[\r\n]", ms)))
                      for ms in strings]
            visible_widths = [maxwidth - (w - l)
                              for w, l in zip(s_widths, s_lens)]
            # wcswidth and _visible_width don't count invisible characters;
            # padfn doesn't need to apply another correction
            padded_strings = ["\n".join([padfn(w, s) for s in (ms.splitlines() or ms)])
                              for ms, w in zip(strings, visible_widths)]
    else:  # single-line cell values
        if not enable_widechars and not has_invisible:
            padded_strings = [padfn(maxwidth, s) for s in strings]
        else:
            # enable wide-character width corrections
            s_lens = list(map(len, strings))
            visible_widths = [maxwidth - (w - l)
                              for w, l in zip(s_widths, s_lens)]
            # wcswidth and _visible_width don't count invisible characters;
            # padfn doesn't need to apply another correction
            padded_strings = [
                padfn(
                    w, s) for s, w in zip(
                    strings, visible_widths)]
    return padded_strings
1236091
function alignLeft(str, len, ch) {
    return str + new Array(len - str.length + 1).join(ch || " ");
}
644924
def _AlignDecodedDataOffset(self, decoded_data_offset):
    
    self._file_object.seek(0, os.SEEK_SET)

    self._decoder = self._GetDecoder()
    self._decoded_data = b''

    encoded_data_offset = 0
    encoded_data_size = self._file_object.get_size()

    while encoded_data_offset < encoded_data_size:
      read_count = self._ReadEncodedData(self._ENCODED_DATA_BUFFER_SIZE)
      if read_count == 0:
        break

      encoded_data_offset += read_count

      if decoded_data_offset < self._decoded_data_size:
        self._decoded_data_offset = decoded_data_offset
        break

      decoded_data_offset -= self._decoded_data_size
1050971
void align() throws IOException {
        for (int i = 0; i < lmargin; i++) out.write(" ");
    }

    /** Increase left margin by indentation width.
     */
    void indent() {
        lmargin = lmargin + width;
    }

    /** Decrease left margin by indentation width.
     */
    void undent() {
        lmargin = lmargin - width;
    }

    /** Enter a new precedence level. Emit a `(' if new precedence level
     *  is less than precedence level so far.
     *  @param contextPrec    The precedence level in force so far.
     *  @param ownPrec        The new precedence level.
     */
    void open(int contextPrec, int ownPrec) throws IOException {
        if (ownPrec < contextPrec) out.write("(");
    }

    /** Leave precedence level. Emit a `(' if inner precedence level
     *  is less than precedence level we revert to.
     *  @param contextPrec    The precedence level we revert to.
     *  @param ownPrec        The inner precedence level.
     */
    void close(int contextPrec, int ownPrec) throws IOException {
        if (ownPrec < contextPrec) out.write(")");
    }

    /** Print string, replacing all non-ascii character with unicode escapes.
     */
    public void print(Object s) throws IOException {
        out.write(Convert.escapeUnicode(s.toString()));
    }

    /** Print new line.
     */
    public void println() throws IOException {
        out.write(lineSep);
    }

    public static String toSimpleString(JCTree tree) {
        return toSimpleString(tree, PREFERRED_LENGTH);
    }

    public static String toSimpleString(JCTree tree, int maxLength) {
        StringWriter s = new StringWriter();
        try {
            new Pretty(s, false).printExpr(tree);
        }
        catch (IOException e) {
            // should never happen, because StringWriter is defined
            // never to throw any IOExceptions
            throw new AssertionError(e);
        }
        //we need to (i) replace all line terminators with a space and (ii) remove
        //occurrences of 'missing' in the Pretty output (generated when types are missing)
        String res = s.toString().trim().replaceAll("\\s+", " ").replaceAll("/\\*missing\\*/", "");
        if (res.length() < maxLength) {
            return res;
        } else {
            int head = (maxLength - trimSequence.length()) * 2 / 3;
            int tail = maxLength - trimSequence.length() - head;
            return res.substring(0, head) + trimSequence + res.substring(res.length() - tail);
        }
    }

    String lineSep = System.getProperty("line.separator");

    /**************************************************************************
     * Traversal methods
     *************************************************************************/

    /** Exception to propogate IOException through visitXXX methods */
    private static class UncheckedIOException extends Error {
        static final long serialVersionUID = -4032692679158424751L;
        UncheckedIOException(IOException e) {
            super(e.getMessage(), e);
        }
    }

    /** Visitor argument: the current precedence level.
     */
    int prec;

    /** Visitor method: print expression tree.
     *  @param prec  The current precedence level.
     */
    public void printExpr(JCTree tree, int prec) throws IOException {
        int prevPrec = this.prec;
        try {
            this.prec = prec;
            if (tree == null) print("/*missing*/");
            else {
                tree.accept(this);
            }
        } catch (UncheckedIOException ex) {
            IOException e = new IOException(ex.getMessage());
            e.initCause(ex);
            throw e;
        } finally {
            this.prec = prevPrec;
        }
    }

    /** Derived visitor method: print expression tree at minimum precedence level
     *  for expression.
     */
    public void printExpr(JCTree tree) throws IOException {
        printExpr(tree, TreeInfo.noPrec);
    }

    /** Derived visitor method: print statement tree.
     */
    public void printStat(JCTree tree) throws IOException {
        printExpr(tree, TreeInfo.notExpression);
    }

    /** Derived visitor method: print list of expression trees, separated by given string.
     *  @param sep the separator string
     */
    public <T extends JCTree> void printExprs(List<T> trees, String sep) throws IOException {
        if (trees.nonEmpty()) {
            printExpr(trees.head);
            for (List<T> l = trees.tail; l.nonEmpty(); l = l.tail) {
                print(sep);
                printExpr(l.head);
            }
        }
    }

    /** Derived visitor method: print list of expression trees, separated by commas.
     */
    public <T extends JCTree> void printExprs(List<T> trees) throws IOException {
        printExprs(trees, ", ");
    }

    /** Derived visitor method: print list of statements, each on a separate line.
     */
    public void printStats(List<? extends JCTree> trees) throws IOException {
        for (List<? extends JCTree> l = trees; l.nonEmpty(); l = l.tail) {
            align();
            printStat(l.head);
            println();
        }
    }

    /** Print a set of modifiers.
     */
    public void printFlags(long flags) throws IOException {
        if ((flags & SYNTHETIC) != 0) print("/*synthetic*/ ");
        print(TreeInfo.flagNames(flags));
        if ((flags & ExtendedStandardFlags) != 0) print(" ");
        if ((flags & ANNOTATION) != 0) print("@");
    }

    public void printAnnotations(List<JCAnnotation> trees) throws IOException {
        for (List<JCAnnotation> l = trees; l.nonEmpty(); l = l.tail) {
            printStat(l.head);
            println();
            align();
        }
    }

    public void printTypeAnnotations(List<JCAnnotation> trees) throws IOException {
        for (List<JCAnnotation> l = trees; l.nonEmpty(); l = l.tail) {
            printExpr(l.head);
            print(" ");
        }
    }

    /** Print documentation comment, if it exists
     *  @param tree    The tree for which a documentation comment should be printed.
     */
    public void printDocComment(JCTree tree) throws IOException {
        if (docComments != null) {
            String dc = docComments.getCommentText(tree);
            if (dc != null) {
                print("/**"); println();
                int pos = 0;
                int endpos = lineEndPos(dc, pos);
                while (pos < dc.length()) {
                    align();
                    print(" *");
                    if (pos < dc.length() && dc.charAt(pos) > ' ') print(" ");
                    print(dc.substring(pos, endpos)); println();
                    pos = endpos + 1;
                    endpos = lineEndPos(dc, pos);
                }
                align(); print(" */"); println();
                align();
            }
        }
    }
//where
    static int lineEndPos(String s, int start) {
        int pos = s.indexOf('\n', start);
        if (pos < 0) pos = s.length();
        return pos;
    }

    /** If type parameter list is non-empty, print it enclosed in
     *  {@literal "<...>"} brackets.
     */
    public void printTypeParameters(List<JCTypeParameter> trees) throws IOException {
        if (trees.nonEmpty()) {
            print("<");
            printExprs(trees);
            print(">");
        }
    }

    /** Print a block.
     */
    public void printBlock(List<? extends JCTree> stats) throws IOException {
        print("{");
        println();
        indent();
        printStats(stats);
        undent();
        align();
        print("}");
    }

    /** Print a block.
     */
    public void printEnumBody(List<JCTree> stats) throws IOException {
        print("{");
        println();
        indent();
        boolean first = true;
        for (List<JCTree> l = stats; l.nonEmpty(); l = l.tail) {
            if (isEnumerator(l.head)) {
                if (!first) {
                    print(",");
                    println();
                }
                align();
                printStat(l.head);
                first = false;
            }
        }
        print(";");
        println();
        for (List<JCTree> l = stats; l.nonEmpty(); l = l.tail) {
            if (!isEnumerator(l.head)) {
                align();
                printStat(l.head);
                println();
            }
        }
        undent();
        align();
        print("}");
    }

    /** Is the given tree an enumerator definition? */
    boolean isEnumerator(JCTree t) {
        return t.hasTag(VARDEF) && (((JCVariableDecl) t).mods.flags & ENUM) != 0;
    }

    /** Print unit consisting of package clause and import statements in toplevel,
     *  followed by class definition. if class definition == null,
     *  print all definitions in toplevel.
     *  @param tree     The toplevel tree
     *  @param cdef     The class definition, which is assumed to be part of the
     *                  toplevel tree.
     */
    public void printUnit(JCCompilationUnit tree, JCClassDecl cdef) throws IOException {
        docComments = tree.docComments;
        printDocComment(tree);

        boolean firstImport = true;
        for (List<JCTree> l = tree.defs;
             l.nonEmpty() &&
                 (cdef == null ||
                  l.head.hasTag(IMPORT) || l.head.hasTag(PACKAGEDEF));
             l = l.tail) {
            if (l.head.hasTag(IMPORT)) {
                JCImport imp = (JCImport)l.head;
                Name name = TreeInfo.name(imp.qualid);
                if (name == name.table.names.asterisk ||
                        cdef == null ||
                        isUsed(TreeInfo.symbol(imp.qualid), cdef)) {
                    if (firstImport) {
                        firstImport = false;
                        println();
                    }
                    printStat(imp);
                }
            } else {
                printStat(l.head);
            }
        }
        if (cdef != null) {
            printStat(cdef);
            println();
        }
    }
    // where
    boolean isUsed(final Symbol t, JCTree cdef) {
        class UsedVisitor extends TreeScanner {
            public void scan(JCTree tree) {
                if (tree!=null && !result) tree.accept(this);
            }
            boolean result = false;
            public void visitIdent(JCIdent tree) {
                if (tree.sym == t) result = true;
            }
        }
        UsedVisitor v = new UsedVisitor();
        v.scan(cdef);
        return v.result;
    }

    /**************************************************************************
     * Visitor methods
     *************************************************************************/

    public void visitTopLevel(JCCompilationUnit tree) {
        try {
            printUnit(tree, null);
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitPackageDef(JCPackageDecl tree) {
        try {
            printDocComment(tree);
            printAnnotations(tree.annotations);
            if (tree.pid != null) {
                print("package ");
                printExpr(tree.pid);
                print(";");
                println();
            }
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    @Override
    public void visitModuleDef(JCModuleDecl tree) {
        try {
            printDocComment(tree);
            printAnnotations(tree.mods.annotations);
            if (tree.getModuleType() == ModuleKind.OPEN) {
                print("open ");
            }
            print("module ");
            printExpr(tree.qualId);
            if (tree.directives == null) {
                print(";");
            } else {
                printBlock(tree.directives);
            }
            println();
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    @Override
    public void visitExports(JCExports tree) {
        try {
            print("exports ");
            printExpr(tree.qualid);
            if (tree.moduleNames != null) {
                print(" to ");
                printExprs(tree.moduleNames);
            }
            print(";");
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    @Override
    public void visitOpens(JCOpens tree) {
        try {
            print("opens ");
            printExpr(tree.qualid);
            if (tree.moduleNames != null) {
                print(" to ");
                printExprs(tree.moduleNames);
            }
            print(";");
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    @Override
    public void visitProvides(JCProvides tree) {
        try {
            print("provides ");
            printExpr(tree.serviceName);
            print(" with ");
            printExprs(tree.implNames);
            print(";");
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    @Override
    public void visitRequires(JCRequires tree) {
        try {
            print("requires ");
            if (tree.isStaticPhase)
                print("static ");
            if (tree.isTransitive)
                print("transitive ");
            printExpr(tree.moduleName);
            print(";");
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    @Override
    public void visitUses(JCUses tree) {
        try {
            print("uses ");
            printExpr(tree.qualid);
            print(";");
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitImport(JCImport tree) {
        try {
            print("import ");
            if (tree.staticImport) print("static ");
            printExpr(tree.qualid);
            print(";");
            println();
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitClassDef(JCClassDecl tree) {
        try {
            println(); align();
            printDocComment(tree);
            printAnnotations(tree.mods.annotations);
            printFlags(tree.mods.flags & ~INTERFACE);
            Name enclClassNamePrev = enclClassName;
            enclClassName = tree.name;
            if ((tree.mods.flags & INTERFACE) != 0) {
                print("interface " + tree.name);
                printTypeParameters(tree.typarams);
                if (tree.implementing.nonEmpty()) {
                    print(" extends ");
                    printExprs(tree.implementing);
                }
            } else {
                if ((tree.mods.flags & ENUM) != 0)
                    print("enum " + tree.name);
                else
                    print("class " + tree.name);
                printTypeParameters(tree.typarams);
                if (tree.extending != null) {
                    print(" extends ");
                    printExpr(tree.extending);
                }
                if (tree.implementing.nonEmpty()) {
                    print(" implements ");
                    printExprs(tree.implementing);
                }
            }
            print(" ");
            if ((tree.mods.flags & ENUM) != 0) {
                printEnumBody(tree.defs);
            } else {
                printBlock(tree.defs);
            }
            enclClassName = enclClassNamePrev;
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitMethodDef(JCMethodDecl tree) {
        try {
            // when producing source output, omit anonymous constructors
            if (tree.name == tree.name.table.names.init &&
                    enclClassName == null &&
                    sourceOutput) return;
            println(); align();
            printDocComment(tree);
            printExpr(tree.mods);
            printTypeParameters(tree.typarams);
            if (tree.name == tree.name.table.names.init) {
                print(enclClassName != null ? enclClassName : tree.name);
            } else {
                printExpr(tree.restype);
                print(" " + tree.name);
            }
            print("(");
            if (tree.recvparam!=null) {
                printExpr(tree.recvparam);
                if (tree.params.size() > 0) {
                    print(", ");
                }
            }
            printExprs(tree.params);
            print(")");
            if (tree.thrown.nonEmpty()) {
                print(" throws ");
                printExprs(tree.thrown);
            }
            if (tree.defaultValue != null) {
                print(" default ");
                printExpr(tree.defaultValue);
            }
            if (tree.body != null) {
                print(" ");
                printStat(tree.body);
            } else {
                print(";");
            }
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitVarDef(JCVariableDecl tree) {
        try {
            if (docComments != null && docComments.hasComment(tree)) {
                println(); align();
            }
            printDocComment(tree);
            if ((tree.mods.flags & ENUM) != 0) {
                print("/*public static final*/ ");
                print(tree.name);
                if (tree.init != null) {
                    if (sourceOutput && tree.init.hasTag(NEWCLASS)) {
                        print(" /*enum*/ ");
                        JCNewClass init = (JCNewClass) tree.init;
                        if (init.args != null && init.args.nonEmpty()) {
                            print("(");
                            print(init.args);
                            print(")");
                        }
                        if (init.def != null && init.def.defs != null) {
                            print(" ");
                            printBlock(init.def.defs);
                        }
                        return;
                    }
                    print(" /* = ");
                    printExpr(tree.init);
                    print(" */");
                }
            } else {
                printExpr(tree.mods);
                if ((tree.mods.flags & VARARGS) != 0) {
                    JCTree vartype = tree.vartype;
                    List<JCAnnotation> tas = null;
                    if (vartype instanceof JCAnnotatedType) {
                        tas = ((JCAnnotatedType)vartype).annotations;
                        vartype = ((JCAnnotatedType)vartype).underlyingType;
                    }
                    printExpr(((JCArrayTypeTree) vartype).elemtype);
                    if (tas != null) {
                        print(' ');
                        printTypeAnnotations(tas);
                    }
                    print("... " + tree.name);
                } else {
                    printExpr(tree.vartype);
                    print(" " + tree.name);
                }
                if (tree.init != null) {
                    print(" = ");
                    printExpr(tree.init);
                }
                if (prec == TreeInfo.notExpression) print(";");
            }
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitSkip(JCSkip tree) {
        try {
            print(";");
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitBlock(JCBlock tree) {
        try {
            printFlags(tree.flags);
            printBlock(tree.stats);
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitDoLoop(JCDoWhileLoop tree) {
        try {
            print("do ");
            printStat(tree.body);
            align();
            print(" while ");
            if (tree.cond.hasTag(PARENS)) {
                printExpr(tree.cond);
            } else {
                print("(");
                printExpr(tree.cond);
                print(")");
            }
            print(";");
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitWhileLoop(JCWhileLoop tree) {
        try {
            print("while ");
            if (tree.cond.hasTag(PARENS)) {
                printExpr(tree.cond);
            } else {
                print("(");
                printExpr(tree.cond);
                print(")");
            }
            print(" ");
            printStat(tree.body);
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitForLoop(JCForLoop tree) {
        try {
            print("for (");
            if (tree.init.nonEmpty()) {
                if (tree.init.head.hasTag(VARDEF)) {
                    printExpr(tree.init.head);
                    for (List<JCStatement> l = tree.init.tail; l.nonEmpty(); l = l.tail) {
                        JCVariableDecl vdef = (JCVariableDecl)l.head;
                        print(", " + vdef.name);
                        if (vdef.init != null) {
                            print(" = ");
                            printExpr(vdef.init);
                        }
                    }
                } else {
                    printExprs(tree.init);
                }
            }
            print("; ");
            if (tree.cond != null) printExpr(tree.cond);
            print("; ");
            printExprs(tree.step);
            print(") ");
            printStat(tree.body);
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitForeachLoop(JCEnhancedForLoop tree) {
        try {
            print("for (");
            printExpr(tree.var);
            print(" : ");
            printExpr(tree.expr);
            print(") ");
            printStat(tree.body);
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitLabelled(JCLabeledStatement tree) {
        try {
            print(tree.label + ": ");
            printStat(tree.body);
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitSwitch(JCSwitch tree) {
        try {
            print("switch ");
            if (tree.selector.hasTag(PARENS)) {
                printExpr(tree.selector);
            } else {
                print("(");
                printExpr(tree.selector);
                print(")");
            }
            print(" {");
            println();
            printStats(tree.cases);
            align();
            print("}");
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitCase(JCCase tree) {
        try {
            if (tree.pat == null) {
                print("default");
            } else {
                print("case ");
                printExpr(tree.pat);
            }
            print(": ");
            println();
            indent();
            printStats(tree.stats);
            undent();
            align();
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitSynchronized(JCSynchronized tree) {
        try {
            print("synchronized ");
            if (tree.lock.hasTag(PARENS)) {
                printExpr(tree.lock);
            } else {
                print("(");
                printExpr(tree.lock);
                print(")");
            }
            print(" ");
            printStat(tree.body);
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitTry(JCTry tree) {
        try {
            print("try ");
            if (tree.resources.nonEmpty()) {
                print("(");
                boolean first = true;
                for (JCTree var : tree.resources) {
                    if (!first) {
                        println();
                        indent();
                    }
                    printStat(var);
                    first = false;
                }
                print(") ");
            }
            printStat(tree.body);
            for (List<JCCatch> l = tree.catchers; l.nonEmpty(); l = l.tail) {
                printStat(l.head);
            }
            if (tree.finalizer != null) {
                print(" finally ");
                printStat(tree.finalizer);
            }
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitCatch(JCCatch tree) {
        try {
            print(" catch (");
            printExpr(tree.param);
            print(") ");
            printStat(tree.body);
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitConditional(JCConditional tree) {
        try {
            open(prec, TreeInfo.condPrec);
            printExpr(tree.cond, TreeInfo.condPrec + 1);
            print(" ? ");
            printExpr(tree.truepart);
            print(" : ");
            printExpr(tree.falsepart, TreeInfo.condPrec);
            close(prec, TreeInfo.condPrec);
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitIf(JCIf tree) {
        try {
            print("if ");
            if (tree.cond.hasTag(PARENS)) {
                printExpr(tree.cond);
            } else {
                print("(");
                printExpr(tree.cond);
                print(")");
            }
            print(" ");
            printStat(tree.thenpart);
            if (tree.elsepart != null) {
                print(" else ");
                printStat(tree.elsepart);
            }
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitExec(JCExpressionStatement tree) {
        try {
            printExpr(tree.expr);
            if (prec == TreeInfo.notExpression) print(";");
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitBreak(JCBreak tree) {
        try {
            print("break");
            if (tree.label != null) print(" " + tree.label);
            print(";");
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitContinue(JCContinue tree) {
        try {
            print("continue");
            if (tree.label != null) print(" " + tree.label);
            print(";");
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitReturn(JCReturn tree) {
        try {
            print("return");
            if (tree.expr != null) {
                print(" ");
                printExpr(tree.expr);
            }
            print(";");
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitThrow(JCThrow tree) {
        try {
            print("throw ");
            printExpr(tree.expr);
            print(";");
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitAssert(JCAssert tree) {
        try {
            print("assert ");
            printExpr(tree.cond);
            if (tree.detail != null) {
                print(" : ");
                printExpr(tree.detail);
            }
            print(";");
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitApply(JCMethodInvocation tree) {
        try {
            if (!tree.typeargs.isEmpty()) {
                if (tree.meth.hasTag(SELECT)) {
                    JCFieldAccess left = (JCFieldAccess)tree.meth;
                    printExpr(left.selected);
                    print(".<");
                    printExprs(tree.typeargs);
                    print(">" + left.name);
                } else {
                    print("<");
                    printExprs(tree.typeargs);
                    print(">");
                    printExpr(tree.meth);
                }
            } else {
                printExpr(tree.meth);
            }
            print("(");
            printExprs(tree.args);
            print(")");
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitNewClass(JCNewClass tree) {
        try {
            if (tree.encl != null) {
                printExpr(tree.encl);
                print(".");
            }
            print("new ");
            if (!tree.typeargs.isEmpty()) {
                print("<");
                printExprs(tree.typeargs);
                print(">");
            }
            if (tree.def != null && tree.def.mods.annotations.nonEmpty()) {
                printTypeAnnotations(tree.def.mods.annotations);
            }
            printExpr(tree.clazz);
            print("(");
            printExprs(tree.args);
            print(")");
            if (tree.def != null) {
                Name enclClassNamePrev = enclClassName;
                enclClassName =
                        tree.def.name != null ? tree.def.name :
                            tree.type != null && tree.type.tsym.name != tree.type.tsym.name.table.names.empty
                                ? tree.type.tsym.name : null;
                if ((tree.def.mods.flags & Flags.ENUM) != 0) print("/*enum*/");
                printBlock(tree.def.defs);
                enclClassName = enclClassNamePrev;
            }
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitNewArray(JCNewArray tree) {
        try {
            if (tree.elemtype != null) {
                print("new ");
                JCTree elem = tree.elemtype;
                printBaseElementType(elem);

                if (!tree.annotations.isEmpty()) {
                    print(' ');
                    printTypeAnnotations(tree.annotations);
                }
                if (tree.elems != null) {
                    print("[]");
                }

                int i = 0;
                List<List<JCAnnotation>> da = tree.dimAnnotations;
                for (List<JCExpression> l = tree.dims; l.nonEmpty(); l = l.tail) {
                    if (da.size() > i && !da.get(i).isEmpty()) {
                        print(' ');
                        printTypeAnnotations(da.get(i));
                    }
                    print("[");
                    i++;
                    printExpr(l.head);
                    print("]");
                }
                printBrackets(elem);
            }
            if (tree.elems != null) {
                print("{");
                printExprs(tree.elems);
                print("}");
            }
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitLambda(JCLambda tree) {
        try {
            print("(");
            if (tree.paramKind == JCLambda.ParameterKind.EXPLICIT) {
                printExprs(tree.params);
            } else {
                String sep = "";
                for (JCVariableDecl param : tree.params) {
                    print(sep);
                    print(param.name);
                    sep = ",";
                }
            }
            print(")->");
            printExpr(tree.body);
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitParens(JCParens tree) {
        try {
            print("(");
            printExpr(tree.expr);
            print(")");
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitAssign(JCAssign tree) {
        try {
            open(prec, TreeInfo.assignPrec);
            printExpr(tree.lhs, TreeInfo.assignPrec + 1);
            print(" = ");
            printExpr(tree.rhs, TreeInfo.assignPrec);
            close(prec, TreeInfo.assignPrec);
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public String operatorName(JCTree.Tag tag) {
        switch(tag) {
            case POS:     return "+";
            case NEG:     return "-";
            case NOT:     return "!";
            case COMPL:   return "~";
            case PREINC:  return "++";
            case PREDEC:  return "--";
            case POSTINC: return "++";
            case POSTDEC: return "--";
            case NULLCHK: return "<*nullchk*>";
            case OR:      return "||";
            case AND:     return "&&";
            case EQ:      return "==";
            case NE:      return "!=";
            case LT:      return "<";
            case GT:      return ">";
            case LE:      return "<=";
            case GE:      return ">=";
            case BITOR:   return "|";
            case BITXOR:  return "^";
            case BITAND:  return "&";
            case SL:      return "<<";
            case SR:      return ">>";
            case USR:     return ">>>";
            case PLUS:    return "+";
            case MINUS:   return "-";
            case MUL:     return "*";
            case DIV:     return "/";
            case MOD:     return "%";
            default: throw new Error();
        }
    }

    public void visitAssignop(JCAssignOp tree) {
        try {
            open(prec, TreeInfo.assignopPrec);
            printExpr(tree.lhs, TreeInfo.assignopPrec + 1);
            print(" " + operatorName(tree.getTag().noAssignOp()) + "= ");
            printExpr(tree.rhs, TreeInfo.assignopPrec);
            close(prec, TreeInfo.assignopPrec);
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitUnary(JCUnary tree) {
        try {
            int ownprec = TreeInfo.opPrec(tree.getTag());
            String opname = operatorName(tree.getTag());
            open(prec, ownprec);
            if (!tree.getTag().isPostUnaryOp()) {
                print(opname);
                printExpr(tree.arg, ownprec);
            } else {
                printExpr(tree.arg, ownprec);
                print(opname);
            }
            close(prec, ownprec);
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitBinary(JCBinary tree) {
        try {
            int ownprec = TreeInfo.opPrec(tree.getTag());
            String opname = operatorName(tree.getTag());
            open(prec, ownprec);
            printExpr(tree.lhs, ownprec);
            print(" " + opname + " ");
            printExpr(tree.rhs, ownprec + 1);
            close(prec, ownprec);
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitTypeCast(JCTypeCast tree) {
        try {
            open(prec, TreeInfo.prefixPrec);
            print("(");
            printExpr(tree.clazz);
            print(")");
            printExpr(tree.expr, TreeInfo.prefixPrec);
            close(prec, TreeInfo.prefixPrec);
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitTypeTest(JCInstanceOf tree) {
        try {
            open(prec, TreeInfo.ordPrec);
            printExpr(tree.expr, TreeInfo.ordPrec);
            print(" instanceof ");
            printExpr(tree.clazz, TreeInfo.ordPrec + 1);
            close(prec, TreeInfo.ordPrec);
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitIndexed(JCArrayAccess tree) {
        try {
            printExpr(tree.indexed, TreeInfo.postfixPrec);
            print("[");
            printExpr(tree.index);
            print("]");
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitSelect(JCFieldAccess tree) {
        try {
            printExpr(tree.selected, TreeInfo.postfixPrec);
            print("." + tree.name);
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitReference(JCMemberReference tree) {
        try {
            printExpr(tree.expr);
            print("::");
            if (tree.typeargs != null) {
                print("<");
                printExprs(tree.typeargs);
                print(">");
            }
            print(tree.getMode() == ReferenceMode.INVOKE ? tree.name : "new");
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitIdent(JCIdent tree) {
        try {
            print(tree.name);
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitLiteral(JCLiteral tree) {
        try {
            switch (tree.typetag) {
                case INT:
                    print(tree.value.toString());
                    break;
                case LONG:
                    print(tree.value + "L");
                    break;
                case FLOAT:
                    print(tree.value + "F");
                    break;
                case DOUBLE:
                    print(tree.value.toString());
                    break;
                case CHAR:
                    print("\'" +
                            Convert.quote(
                            String.valueOf((char)((Number)tree.value).intValue())) +
                            "\'");
                    break;
                case BOOLEAN:
                    print(((Number)tree.value).intValue() == 1 ? "true" : "false");
                    break;
                case BOT:
                    print("null");
                    break;
                default:
                    print("\"" + Convert.quote(tree.value.toString()) + "\"");
                    break;
            }
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitTypeIdent(JCPrimitiveTypeTree tree) {
        try {
            switch(tree.typetag) {
                case BYTE:
                    print("byte");
                    break;
                case CHAR:
                    print("char");
                    break;
                case SHORT:
                    print("short");
                    break;
                case INT:
                    print("int");
                    break;
                case LONG:
                    print("long");
                    break;
                case FLOAT:
                    print("float");
                    break;
                case DOUBLE:
                    print("double");
                    break;
                case BOOLEAN:
                    print("boolean");
                    break;
                case VOID:
                    print("void");
                    break;
                default:
                    print("error");
                    break;
            }
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitTypeArray(JCArrayTypeTree tree) {
        try {
            printBaseElementType(tree);
            printBrackets(tree);
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    // Prints the inner element type of a nested array
    private void printBaseElementType(JCTree tree) throws IOException {
        printExpr(TreeInfo.innermostType(tree));
    }

    // prints the brackets of a nested array in reverse order
    // tree is either JCArrayTypeTree or JCAnnotatedTypeTree
    private void printBrackets(JCTree tree) throws IOException {
        JCTree elem = tree;
        while (true) {
            if (elem.hasTag(ANNOTATED_TYPE)) {
                JCAnnotatedType atype = (JCAnnotatedType) elem;
                elem = atype.underlyingType;
                if (elem.hasTag(TYPEARRAY)) {
                    print(' ');
                    printTypeAnnotations(atype.annotations);
                }
            }
            if (elem.hasTag(TYPEARRAY)) {
                print("[]");
                elem = ((JCArrayTypeTree)elem).elemtype;
            } else {
                break;
            }
        }
    }

    public void visitTypeApply(JCTypeApply tree) {
        try {
            printExpr(tree.clazz);
            print("<");
            printExprs(tree.arguments);
            print(">");
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitTypeUnion(JCTypeUnion tree) {
        try {
            printExprs(tree.alternatives, " | ");
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitTypeIntersection(JCTypeIntersection tree) {
        try {
            printExprs(tree.bounds, " & ");
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitTypeParameter(JCTypeParameter tree) {
        try {
            if (tree.annotations.nonEmpty()) {
                this.printTypeAnnotations(tree.annotations);
            }
            print(tree.name);
            if (tree.bounds.nonEmpty()) {
                print(" extends ");
                printExprs(tree.bounds, " & ");
            }
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    @Override
    public void visitWildcard(JCWildcard tree) {
        try {
            print(tree.kind);
            if (tree.kind.kind != BoundKind.UNBOUND)
                printExpr(tree.inner);
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    @Override
    public void visitTypeBoundKind(TypeBoundKind tree) {
        try {
            print(String.valueOf(tree.kind));
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitErroneous(JCErroneous tree) {
        try {
            print("(ERROR)");
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitLetExpr(LetExpr tree) {
        try {
            print("(let " + tree.defs + " in " + tree.expr + ")");
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitModifiers(JCModifiers mods) {
        try {
            printAnnotations(mods.annotations);
            printFlags(mods.flags);
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitAnnotation(JCAnnotation tree) {
        try {
            print("@");
            printExpr(tree.annotationType);
            print("(");
            printExprs(tree.args);
            print(")");
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitAnnotatedType(JCAnnotatedType tree) {
        try {
            if (tree.underlyingType.hasTag(SELECT)) {
                JCFieldAccess access = (JCFieldAccess) tree.underlyingType;
                printExpr(access.selected, TreeInfo.postfixPrec);
                print(".");
                printTypeAnnotations(tree.annotations);
                print(access.name);
            } else if (tree.underlyingType.hasTag(TYPEARRAY)) {
                printBaseElementType(tree);
                printBrackets(tree);
            } else {
                printTypeAnnotations(tree.annotations);
                printExpr(tree.underlyingType);
            }
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    public void visitTree(JCTree tree) {
        try {
            print("(UNKNOWN: " + tree.getTag() + ")");
            println();
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

}
726691
def align(args):
    
    valid_modes = ("bwasw", "aln", "mem")
    p = OptionParser(align.__doc__)
    p.add_option("--mode", default="mem", choices=valid_modes, help="BWA mode")
    set_align_options(p)
    p.set_sam_options()

    opts, args = p.parse_args(args)
    mode = opts.mode
    nargs = len(args)

    if nargs not in (2, 3):
        sys.exit(not p.print_help())

    tag = "bwa-{0}: ".format(mode)
    c = mem
    if nargs == 2:
        tag += "Single-end alignment"
        if mode == "bwasw":
            c = bwasw
        elif mode == "aln":
            c = samse
    else:
        assert mode != "bwasw", "Cannot use --bwasw with paired-end mode"
        tag += "Paired-end alignment"
        if mode == "aln":
            c = sampe

    logging.debug(tag)
    cmd, samfile = c(args, opts)
    if cmd:
        cmd = output_bam(cmd, samfile)

    bam = opts.bam
    unmapped = opts.unmapped

    sh(cmd)
    if unmapped:
        dbfile, readfile = args[:2]
        mopts = [samfile, "--unmapped"]
        if not bam:
            mopts += ["--sam"]
        mapped(mopts)
        FileShredder([samfile])

    return samfile, None
483946
def align(aligner, reads):
    '''
    
    '''
    i = 0
    for record in SeqIO.parse(reads, "fastq"):
        try:
            next(aligner.map(str(record.seq)))
            i += 1
        except StopIteration:
            print(record.format("fastq"), end='')
    sys.stderr.write("NanoLyse: removed {} reads.\n".format(i))
426535
public void alignOutput(int align) throws IOException
    {
        int mod = position % align;
        if (mod > 0)
        {
            skipOutput(align - mod);
        }
    }
915817
def align(value):
        
        if value.value:
            _assert_is_type('shape.value', value.value, str_types)
            if value.value not in PropertySet._valid_align:
                raise ValueError(value.value + ' is not a valid alignment')