Example usage for java.io BufferedReader mark

Introduction

In this page you can find the example usage for java.io BufferedReader mark.

Prototype

public void mark(int readAheadLimit) throws IOException 

Source Link

Document

Marks the present position in the stream.

Usage

From source file:org.eclipse.mylyn.internal.bugzilla.core.BugzillaReportSubmitForm.java

/**
 * Post the bug to the bugzilla server TODO: fix this mess
 */// ww w .  jav a  2 s .com
public String submitReportToRepository(BugzillaClient client)
        throws IOException, BugzillaException, PossibleBugzillaFailureException, GeneralSecurityException {
    NameValuePair[] formData = fields.values().toArray(new NameValuePair[fields.size()]);
    InputStream inputStream = null;
    String result = null;
    PostMethod method = null;
    try {
        if (isNewBugPost()) {
            method = client.postFormData(POST_BUG_CGI, formData);
        } else {
            method = client.postFormData(PROCESS_BUG_CGI, formData);
        }

        if (method == null)
            throw new BugzillaException("Could not post form");

        BufferedReader in = new BufferedReader(new InputStreamReader(method.getResponseBodyAsStream()));
        in.mark(10);
        HtmlStreamTokenizer tokenizer = new HtmlStreamTokenizer(in, null);

        boolean existingBugPosted = false;
        boolean isTitle = false;
        String title = "";
        for (Token token = tokenizer.nextToken(); token.getType() != Token.EOF; token = tokenizer.nextToken()) {

            if (token.getType() == Token.TAG
                    && ((HtmlTag) (token.getValue())).getTagType() == HtmlTag.Type.TITLE
                    && !((HtmlTag) (token.getValue())).isEndTag()) {
                isTitle = true;
                continue;
            }

            if (isTitle) {
                // get all of the data in the title tag
                if (token.getType() != Token.TAG) {
                    title += ((StringBuffer) token.getValue()).toString().toLowerCase() + " ";
                    continue;
                } else if (token.getType() == Token.TAG
                        && ((HtmlTag) token.getValue()).getTagType() == HtmlTag.Type.TITLE
                        && ((HtmlTag) token.getValue()).isEndTag()) {
                    if (!isNewBugPost && (title.toLowerCase().matches(".*bug\\s+processed.*")
                            || title.toLowerCase().matches(".*defect\\s+processed.*"))) {
                        existingBugPosted = true;
                    } else if (isNewBugPost && prefix != null && prefix2 != null && postfix != null
                            && postfix2 != null && result == null) {
                        int startIndex = -1;
                        int startIndexPrefix = title.toLowerCase().indexOf(prefix.toLowerCase());
                        int startIndexPrefix2 = title.toLowerCase().indexOf(prefix2.toLowerCase());

                        if (startIndexPrefix != -1 || startIndexPrefix2 != -1) {
                            if (startIndexPrefix != -1) {
                                startIndex = startIndexPrefix + prefix.length();
                            } else {
                                startIndex = startIndexPrefix2 + prefix2.length();
                            }
                            int stopIndex = title.toLowerCase().indexOf(postfix.toLowerCase(), startIndex);
                            if (stopIndex == -1)
                                stopIndex = title.toLowerCase().indexOf(postfix2.toLowerCase(), startIndex);
                            if (stopIndex > -1) {
                                result = (title.substring(startIndex, stopIndex)).trim();
                            }
                        }
                    }
                    break;
                }
            }
        }

        if ((!isNewBugPost && existingBugPosted != true) || (isNewBugPost && result == null)) {
            in.reset();
            BugzillaClient.parseHtmlError(in);
        }
    } catch (ParseException e) {
        throw new IOException("Could not parse response from server.");
    } finally {
        if (inputStream != null) {
            inputStream.close();
        }
        if (method != null) {
            method.releaseConnection();
        }
    }
    // return the bug number
    return result;
}

---

From source file:ffx.xray.CIFFilter.java

/**
 * {@inheritDoc}//w w w .j  av a2  s. c  o m
 */
@Override
public double getResolution(File cifFile, Crystal crystal) {
    double res = Double.POSITIVE_INFINITY;

    try {
        BufferedReader br = new BufferedReader(new FileReader(cifFile));

        String str;
        int ncol = 0;
        boolean inhkl = false;
        while ((str = br.readLine()) != null) {
            String strarray[] = str.split("\\s+");

            if (strarray[0].startsWith("_refln.")) {
                inhkl = true;
                br.mark(0);
                String cifarray[] = strarray[0].split("\\.+");
                switch (Header.toHeader(cifarray[1])) {
                case index_h:
                    h = ncol;
                    break;
                case index_k:
                    k = ncol;
                    break;
                case index_l:
                    l = ncol;
                    break;
                }

                ncol++;
            } else if (inhkl) {
                if (h < 0 || k < 0 || l < 0) {
                    String message = "Fatal error in CIF file - no H K L indexes?\n";
                    logger.log(Level.SEVERE, message);
                    return -1.0;
                }
                break;
            }
        }

        // go back to where the reflections start
        br.reset();
        HKL hkl = new HKL();
        while ((str = br.readLine()) != null) {
            // reached end, break
            if (str.trim().startsWith("#END")) {
                break;
            } else if (str.trim().startsWith("data")) {
                break;
            } else if (str.trim().startsWith("#")) {
                continue;
            }

            String strarray[] = str.trim().split("\\s+");
            // some files split data on to multiple lines
            while (strarray.length < ncol) {
                str = str + " " + br.readLine();
                strarray = str.trim().split("\\s+");
            }

            int ih = Integer.parseInt(strarray[h]);
            int ik = Integer.parseInt(strarray[k]);
            int il = Integer.parseInt(strarray[l]);

            hkl.h(ih);
            hkl.k(ik);
            hkl.l(il);
            res = Math.min(res, Crystal.res(crystal, hkl));
        }
    } catch (IOException ioe) {
        System.out.println("IO Exception: " + ioe.getMessage());
        return -1.0;
    }

    return res;
}

---

From source file:com.googlecode.erca.framework.io.in.RcftParser.java

private void parseRelationalContext(BufferedReader input, String desc) throws IOException {

    RelationalContext rc = RcfFactory.eINSTANCE.createRelationalContext();
    String rcName = desc.split("\\ ")[1];

    logger.info("Parsing relational context " + rcName);

    rc.setName(rcName);/*from   w  w w .ja  v  a  2 s .  c o m*/

    String source = input.readLine().trim().split("\\ ")[1];
    String target = input.readLine().trim().split("\\ ")[1];
    String sclOp = input.readLine().trim().split("\\ ")[1];
    FormalContext sourceFc = rcf.getFormalContext(source);
    FormalContext targetFc = rcf.getFormalContext(target);
    rc.setSourceContext(sourceFc);
    rc.setTargetContext(targetFc);
    rc.setScalingOperator(sclOp);

    input.mark(0);

    String line = input.readLine();
    int currentRow = 0;
    Map<Integer, Entity> tgtEnts = new HashMap<Integer, Entity>();

    while (line != null) {

        String tline = line.trim();
        if (tline.startsWith("RelationalContext"))
            break;
        else if (tline.startsWith("FormalContext"))
            break;
        else if (tline.equals(""))
            break;

        String[] tokens = line.split("\\|");
        int len = tokens.length;
        if (currentRow == 0) {

            for (int i = 2; i < len; i++) {
                String name = tokens[i].trim();
                Entity ent = targetFc.getEntity(name);
                tgtEnts.put(i, ent);
            }

        } else {
            String name = tokens[1].trim();
            Entity srcEnt = sourceFc.getEntity(name);

            for (int i = 2; i < len; i++) {
                String cell = tokens[i].trim().toLowerCase();
                if ("x".equals(cell)) {
                    Entity tgtEnt = tgtEnts.get(i);
                    Pair pair = RcfFactory.eINSTANCE.createPair();
                    pair.setSource(srcEnt);
                    pair.setTarget(tgtEnt);
                    rc.getRelation().add(pair);

                    logger.debug("Creates pair between " + srcEnt.getName() + " and " + tgtEnt.getName()
                            + ". Line: " + currentRow);
                }
            }
        }

        currentRow++;

        input.mark(0);

        line = input.readLine();
    }

    rcf.getRelationalContexts().add(rc);

    if (line != null)
        input.reset();

}

---

From source file:ffx.xray.parsers.CIFFilter.java

/**
 * {@inheritDoc}/*from  w  ww  . jav  a2s  .com*/
 */
@Override
public double getResolution(File cifFile, Crystal crystal) {

    double resolution = Double.POSITIVE_INFINITY;

    try {
        BufferedReader br = new BufferedReader(new FileReader(cifFile));
        String string;
        int nCol = 0;
        boolean inHKL = false;
        while ((string = br.readLine()) != null) {
            String strArray[] = string.split("\\s+");
            if (strArray[0].startsWith("_refln.")) {
                inHKL = true;
                br.mark(0);
                String cifArray[] = strArray[0].split("\\.+");
                switch (Header.toHeader(cifArray[1])) {
                case index_h:
                    h = nCol;
                    break;
                case index_k:
                    k = nCol;
                    break;
                case index_l:
                    l = nCol;
                    break;
                }
                nCol++;
            } else if (inHKL) {
                if (h < 0 || k < 0 || l < 0) {
                    String message = " Fatal error in CIF file - no H K L indexes?\n";
                    logger.log(Level.SEVERE, message);
                    return -1.0;
                }
                break;
            }
        }

        // Go back to where the reflections start.
        br.reset();
        HKL hkl = new HKL();
        while ((string = br.readLine()) != null) {

            // Reached end, break.
            if (string.trim().startsWith("#END")) {
                break;
            } else if (string.trim().startsWith("data")) {
                break;
            } else if (string.trim().startsWith("#")) {
                continue;
            }

            // Some files split data on to multiple lines.
            String strArray[] = string.trim().split("\\s+");
            while (strArray.length < nCol) {
                string = string + " " + br.readLine();
                strArray = string.trim().split("\\s+");
            }

            int ih = Integer.parseInt(strArray[h]);
            int ik = Integer.parseInt(strArray[k]);
            int il = Integer.parseInt(strArray[l]);

            hkl.h(ih);
            hkl.k(ik);
            hkl.l(il);
            resolution = min(resolution, Crystal.res(crystal, hkl));
        }
    } catch (IOException e) {
        String message = " CIF IO Exception.";
        logger.log(Level.WARNING, message, e);
        return -1.0;
    }
    return resolution;
}

---

From source file:ffx.xray.CIFFilter.java

/**
 * {@inheritDoc}//  w  ww  . j  av  a2  s . c o  m
 */
@Override
public boolean readFile(File cifFile, ReflectionList reflectionlist, DiffractionRefinementData refinementdata,
        CompositeConfiguration properties) {
    int nread, nnan, nres, nignore, ncifignore, nfriedel, ncut;
    boolean transpose = false;
    boolean intensitiesToAmplitudes = false;

    StringBuilder sb = new StringBuilder();
    sb.append(String.format(" Opening %s\n", cifFile.getName()));
    if (refinementdata.rfreeflag < 0) {
        refinementdata.setFreeRFlag(1);
        sb.append(String.format(" Setting R free flag to CIF default: %d\n", refinementdata.rfreeflag));
    }

    try {
        BufferedReader br = new BufferedReader(new FileReader(cifFile));

        String str;
        int ncol = 0;
        boolean inhkl = false;
        while ((str = br.readLine()) != null) {
            String strarray[] = str.split("\\s+");

            if (strarray[0].startsWith("_refln.")) {
                inhkl = true;
                br.mark(0);
                String cifarray[] = strarray[0].split("\\.+");
                switch (Header.toHeader(cifarray[1])) {
                case index_h:
                    h = ncol;
                    break;
                case index_k:
                    k = ncol;
                    break;
                case index_l:
                    l = ncol;
                    break;
                case F_meas:
                case F_meas_au:
                    fo = ncol;
                    break;
                case F_meas_sigma:
                case F_meas_sigma_au:
                    sigfo = ncol;
                    break;
                case intensity_meas:
                    io = ncol;
                    break;
                case intensity_sigma:
                    sigio = ncol;
                    break;
                case status:
                    rfree = ncol;
                    break;
                }

                ncol++;
            } else if (inhkl) {
                if (h < 0 || k < 0 || l < 0) {
                    String message = "Fatal error in CIF file - no H K L indexes?\n";
                    logger.log(Level.SEVERE, message);
                    return false;
                }
                break;
            }
        }

        if (fo < 0 && sigfo < 0 && io > 0 && sigio > 0) {
            intensitiesToAmplitudes = true;
        }

        if (fo < 0 && io < 0) {
            logger.severe("Reflection data (I/F) not found in CIF file!");
        }

        // go back to where the reflections start
        br.reset();

        // check if HKLs need to be transposed or not
        HKL mate = new HKL();
        int nposignore = 0;
        int ntransignore = 0;
        while ((str = br.readLine()) != null) {
            // reached end, break
            if (str.trim().startsWith("#END")) {
                break;
            } else if (str.trim().startsWith("data")) {
                break;
            } else if (str.trim().startsWith("#")) {
                continue;
            }

            String strarray[] = str.trim().split("\\s+");
            // some files split data on to multiple lines
            while (strarray.length < ncol) {
                str = str + " " + br.readLine();
                strarray = str.trim().split("\\s+");
            }

            if (rfree > 0) {
                // ignored cases
                if (strarray[rfree].charAt(0) == 'x' || strarray[rfree].charAt(0) == '<'
                        || strarray[rfree].charAt(0) == '-' || strarray[rfree].charAt(0) == 'h'
                        || strarray[rfree].charAt(0) == 'l') {
                    continue;
                }
            }
            int ih = Integer.parseInt(strarray[h]);
            int ik = Integer.parseInt(strarray[k]);
            int il = Integer.parseInt(strarray[l]);
            boolean friedel = reflectionlist.findSymHKL(ih, ik, il, mate, false);
            HKL hklpos = reflectionlist.getHKL(mate);
            if (hklpos == null) {
                nposignore++;
            }

            friedel = reflectionlist.findSymHKL(ih, ik, il, mate, true);
            HKL hkltrans = reflectionlist.getHKL(mate);
            if (hkltrans == null) {
                ntransignore++;
            }
        }
        if (nposignore > ntransignore) {
            transpose = true;
        }

        // reopen to start at beginning
        br = new BufferedReader(new FileReader(cifFile));
        inhkl = false;
        while ((str = br.readLine()) != null) {
            String strarray[] = str.split("\\s+");

            if (strarray[0].startsWith("_refln.")) {
                br.mark(0);
                inhkl = true;
            } else if (inhkl) {
                break;
            }
        }

        // go back to where the reflections start
        br.reset();

        // read in data
        double anofsigf[][] = new double[refinementdata.n][4];
        for (int i = 0; i < refinementdata.n; i++) {
            anofsigf[i][0] = anofsigf[i][1] = anofsigf[i][2] = anofsigf[i][3] = Double.NaN;
        }
        nread = nnan = nres = nignore = ncifignore = nfriedel = ncut = 0;
        while ((str = br.readLine()) != null) {
            // reached end, break
            if (str.trim().startsWith("#END")) {
                break;
            } else if (str.trim().startsWith("data")) {
                break;
            } else if (str.trim().startsWith("#")) {
                continue;
            }

            String strarray[] = str.trim().split("\\s+");
            // some files split data on to multiple lines
            while (strarray.length < ncol) {
                str = str + " " + br.readLine();
                strarray = str.trim().split("\\s+");
            }

            int ih = Integer.parseInt(strarray[h]);
            int ik = Integer.parseInt(strarray[k]);
            int il = Integer.parseInt(strarray[l]);
            boolean friedel = reflectionlist.findSymHKL(ih, ik, il, mate, transpose);
            HKL hkl = reflectionlist.getHKL(mate);

            if (hkl != null) {
                boolean isnull = false;

                if (rfree > 0) {
                    if (strarray[rfree].charAt(0) == 'o') {
                        refinementdata.setFreeR(hkl.index(), 0);
                    } else if (strarray[rfree].charAt(0) == 'f') {
                        refinementdata.setFreeR(hkl.index(), 1);
                    } else if (strarray[rfree].charAt(0) == 'x') {
                        isnull = true;
                        nnan++;
                    } else if (strarray[rfree].charAt(0) == '<' || strarray[rfree].charAt(0) == '-'
                            || strarray[rfree].charAt(0) == 'h' || strarray[rfree].charAt(0) == 'l') {
                        isnull = true;
                        ncifignore++;
                    } else {
                        refinementdata.setFreeR(hkl.index(), Integer.parseInt(strarray[rfree]));
                    }
                }

                if (!intensitiesToAmplitudes && !isnull) {
                    if (strarray[fo].charAt(0) == '?' || strarray[sigfo].charAt(0) == '?') {
                        isnull = true;
                        nnan++;
                        continue;
                    }

                    if (refinementdata.fsigfcutoff > 0.0) {
                        double f1 = Double.parseDouble(strarray[fo]);
                        double sigf1 = Double.parseDouble(strarray[sigfo]);
                        if ((f1 / sigf1) < refinementdata.fsigfcutoff) {
                            ncut++;
                            continue;
                        }
                    }

                    if (friedel) {
                        anofsigf[hkl.index()][2] = Double.parseDouble(strarray[fo]);
                        anofsigf[hkl.index()][3] = Double.parseDouble(strarray[sigfo]);
                        nfriedel++;
                    } else {
                        anofsigf[hkl.index()][0] = Double.parseDouble(strarray[fo]);
                        anofsigf[hkl.index()][1] = Double.parseDouble(strarray[sigfo]);
                    }
                }

                if (intensitiesToAmplitudes && !isnull) {
                    if (strarray[io].charAt(0) == '?' || strarray[sigio].charAt(0) == '?') {
                        isnull = true;
                        nnan++;
                        continue;
                    }

                    if (friedel) {
                        anofsigf[hkl.index()][2] = Double.parseDouble(strarray[io]);
                        anofsigf[hkl.index()][3] = Double.parseDouble(strarray[sigio]);
                        nfriedel++;
                    } else {
                        anofsigf[hkl.index()][0] = Double.parseDouble(strarray[io]);
                        anofsigf[hkl.index()][1] = Double.parseDouble(strarray[sigio]);
                    }
                }

                nread++;
            } else {
                HKL tmp = new HKL(ih, ik, il);
                if (!reflectionlist.resolution
                        .inInverseResSqRange(Crystal.invressq(reflectionlist.crystal, tmp))) {
                    nres++;
                } else {
                    nignore++;
                }
            }
        }

        br.close();

        // set up fsigf from F+ and F-
        refinementdata.generate_fsigf_from_anofsigf(anofsigf);

        if (intensitiesToAmplitudes) {
            refinementdata.intensities_to_amplitudes();
        }
    } catch (IOException ioe) {
        System.out.println("IO Exception: " + ioe.getMessage());
        return false;
    }

    sb.append(String.format(" HKL data is %s\n", transpose ? "transposed" : "not transposed"));
    sb.append(String.format(" HKL read in:                             %d\n", nread));
    sb.append(String.format(" HKL read as friedel mates:               %d\n", nfriedel));
    sb.append(String.format(" HKL with NaN (ignored):                  %d\n", nnan));
    sb.append(String.format(" HKL NOT read in (status <, -, h or l):   %d\n", ncifignore));
    sb.append(String.format(" HKL NOT read in (too high resolution):   %d\n", nres));
    sb.append(String.format(" HKL NOT read in (not in internal list?): %d\n", nignore));
    sb.append(String.format(" HKL NOT read in (F/sigF cutoff):         %d\n", ncut));
    sb.append(String.format(" HKL in internal list:                    %d\n", reflectionlist.hkllist.size()));
    if (logger.isLoggable(Level.INFO)) {
        logger.info(sb.toString());
    }

    if (rfree < 0) {
        refinementdata.generateRFree();
    }

    return true;
}

---

From source file:ffx.xray.parsers.CIFFilter.java

/**
 * {@inheritDoc}//from  w ww.j a  va 2 s .co  m
 */
@Override
public boolean readFile(File cifFile, ReflectionList reflectionList, DiffractionRefinementData refinementData,
        CompositeConfiguration properties) {

    int nRead, nNAN, nRes;
    int nIgnore, nCIFIgnore;
    int nFriedel, nCut;
    boolean transpose = false;
    boolean intensitiesToAmplitudes = false;

    StringBuilder sb = new StringBuilder();
    sb.append(String.format(" Opening %s\n", cifFile.getName()));
    if (refinementData.rfreeflag < 0) {
        refinementData.setFreeRFlag(1);
        sb.append(format(" Setting R free flag to CIF default: %d\n", refinementData.rfreeflag));
    }

    try {
        BufferedReader br = new BufferedReader(new FileReader(cifFile));

        String string;
        int nCol = 0;
        boolean inHKL = false;
        while ((string = br.readLine()) != null) {
            String stringArray[] = string.split("\\s+");
            if (stringArray[0].startsWith("_refln.")) {
                inHKL = true;
                br.mark(0);
                String cifArray[] = stringArray[0].split("\\.+");
                switch (Header.toHeader(cifArray[1])) {
                case index_h:
                    h = nCol;
                    break;
                case index_k:
                    k = nCol;
                    break;
                case index_l:
                    l = nCol;
                    break;
                case F_meas:
                case F_meas_au:
                    fo = nCol;
                    break;
                case F_meas_sigma:
                case F_meas_sigma_au:
                    sigFo = nCol;
                    break;
                case intensity_meas:
                    io = nCol;
                    break;
                case intensity_sigma:
                    sigIo = nCol;
                    break;
                case status:
                    rFree = nCol;
                    break;
                }
                nCol++;
            } else if (inHKL) {
                if (h < 0 || k < 0 || l < 0) {
                    String message = " Fatal error in CIF file - no H K L indexes?\n";
                    logger.log(Level.SEVERE, message);
                    return false;
                }
                break;
            }
        }

        if (fo < 0 && sigFo < 0 && io > 0 && sigIo > 0) {
            intensitiesToAmplitudes = true;
        }

        if (fo < 0 && io < 0) {
            logger.severe(" Reflection data (I/F) not found in CIF file!");
        }

        // Go back to where the reflections start.
        br.reset();

        // Check if HKLs need to be transposed or not.
        HKL mate = new HKL();
        int nPosIgnore = 0;
        int nTransIgnore = 0;
        while ((string = br.readLine()) != null) {

            if (string.trim().startsWith("#END")) {
                // Reached end, break.
                break;
            } else if (string.trim().startsWith("data")) {
                break;
            } else if (string.trim().startsWith("#")) {
                continue;
            }

            // Some files split data on to multiple lines.
            String strArray[] = string.trim().split("\\s+");
            while (strArray.length < nCol) {
                string = string + " " + br.readLine();
                strArray = string.trim().split("\\s+");
            }

            if (rFree > 0) {
                // Ignored cases.
                if (strArray[rFree].charAt(0) == 'x' || strArray[rFree].charAt(0) == '<'
                        || strArray[rFree].charAt(0) == '-' || strArray[rFree].charAt(0) == 'h'
                        || strArray[rFree].charAt(0) == 'l') {
                    continue;
                }
            }

            int ih = Integer.parseInt(strArray[h]);
            int ik = Integer.parseInt(strArray[k]);
            int il = Integer.parseInt(strArray[l]);

            boolean friedel = reflectionList.findSymHKL(ih, ik, il, mate, false);
            HKL hklPos = reflectionList.getHKL(mate);
            if (hklPos == null) {
                nPosIgnore++;
            }

            friedel = reflectionList.findSymHKL(ih, ik, il, mate, true);
            HKL hklTrans = reflectionList.getHKL(mate);
            if (hklTrans == null) {
                nTransIgnore++;
            }
        }
        if (nPosIgnore > nTransIgnore) {
            transpose = true;
        }

        // Re-open to start at beginning.
        br = new BufferedReader(new FileReader(cifFile));
        inHKL = false;
        while ((string = br.readLine()) != null) {
            String strArray[] = string.split("\\s+");
            if (strArray[0].startsWith("_refln.")) {
                br.mark(0);
                inHKL = true;
            } else if (inHKL) {
                break;
            }
        }

        // Go back to where the reflections start.
        br.reset();

        // Read in data.
        double anofSigF[][] = new double[refinementData.n][4];
        for (int i = 0; i < refinementData.n; i++) {
            anofSigF[i][0] = anofSigF[i][1] = anofSigF[i][2] = anofSigF[i][3] = Double.NaN;
        }
        nRead = nNAN = nRes = nIgnore = nCIFIgnore = nFriedel = nCut = 0;
        while ((string = br.readLine()) != null) {

            // Reached end, break.
            if (string.trim().startsWith("#END")) {
                break;
            } else if (string.trim().startsWith("data")) {
                break;
            } else if (string.trim().startsWith("#")) {
                continue;
            }

            // Some files split data on to multiple lines.
            String strArray[] = string.trim().split("\\s+");
            while (strArray.length < nCol) {
                string = string + " " + br.readLine();
                strArray = string.trim().split("\\s+");
            }

            int ih = Integer.parseInt(strArray[h]);
            int ik = Integer.parseInt(strArray[k]);
            int il = Integer.parseInt(strArray[l]);

            boolean friedel = reflectionList.findSymHKL(ih, ik, il, mate, transpose);
            HKL hkl = reflectionList.getHKL(mate);
            if (hkl != null) {
                boolean isnull = false;
                if (rFree > 0) {
                    if (strArray[rFree].charAt(0) == 'o') {
                        refinementData.setFreeR(hkl.index(), 0);
                    } else if (strArray[rFree].charAt(0) == 'f') {
                        refinementData.setFreeR(hkl.index(), 1);
                    } else if (strArray[rFree].charAt(0) == 'x') {
                        isnull = true;
                        nNAN++;
                    } else if (strArray[rFree].charAt(0) == '<' || strArray[rFree].charAt(0) == '-'
                            || strArray[rFree].charAt(0) == 'h' || strArray[rFree].charAt(0) == 'l') {
                        isnull = true;
                        nCIFIgnore++;
                    } else {
                        refinementData.setFreeR(hkl.index(), Integer.parseInt(strArray[rFree]));
                    }
                }

                if (!intensitiesToAmplitudes && !isnull) {
                    if (strArray[fo].charAt(0) == '?' || strArray[sigFo].charAt(0) == '?') {
                        isnull = true;
                        nNAN++;
                        continue;
                    }

                    if (refinementData.fsigfcutoff > 0.0) {
                        double f1 = Double.parseDouble(strArray[fo]);
                        double sigf1 = Double.parseDouble(strArray[sigFo]);
                        if ((f1 / sigf1) < refinementData.fsigfcutoff) {
                            nCut++;
                            continue;
                        }
                    }

                    if (friedel) {
                        anofSigF[hkl.index()][2] = Double.parseDouble(strArray[fo]);
                        anofSigF[hkl.index()][3] = Double.parseDouble(strArray[sigFo]);
                        nFriedel++;
                    } else {
                        anofSigF[hkl.index()][0] = Double.parseDouble(strArray[fo]);
                        anofSigF[hkl.index()][1] = Double.parseDouble(strArray[sigFo]);
                    }
                }

                if (intensitiesToAmplitudes && !isnull) {
                    if (strArray[io].charAt(0) == '?' || strArray[sigIo].charAt(0) == '?') {
                        isnull = true;
                        nNAN++;
                        continue;
                    }

                    if (friedel) {
                        anofSigF[hkl.index()][2] = Double.parseDouble(strArray[io]);
                        anofSigF[hkl.index()][3] = Double.parseDouble(strArray[sigIo]);
                        nFriedel++;
                    } else {
                        anofSigF[hkl.index()][0] = Double.parseDouble(strArray[io]);
                        anofSigF[hkl.index()][1] = Double.parseDouble(strArray[sigIo]);
                    }
                }

                nRead++;
            } else {
                HKL tmp = new HKL(ih, ik, il);
                if (!reflectionList.resolution
                        .inInverseResSqRange(Crystal.invressq(reflectionList.crystal, tmp))) {
                    nRes++;
                } else {
                    nIgnore++;
                }
            }
        }
        br.close();

        // Set up fsigf from F+ and F-.
        refinementData.generate_fsigf_from_anofsigf(anofSigF);
        if (intensitiesToAmplitudes) {
            refinementData.intensities_to_amplitudes();
        }
    } catch (IOException ioe) {
        System.out.println("IO Exception: " + ioe.getMessage());
        return false;
    }

    sb.append(String.format(" HKL data is %s\n", transpose ? "transposed" : "not transposed"));
    sb.append(String.format(" HKL read in:                             %d\n", nRead));
    sb.append(String.format(" HKL read as friedel mates:               %d\n", nFriedel));
    sb.append(String.format(" HKL with NaN (ignored):                  %d\n", nNAN));
    sb.append(String.format(" HKL NOT read in (status <, -, h or l):   %d\n", nCIFIgnore));
    sb.append(String.format(" HKL NOT read in (too high resolution):   %d\n", nRes));
    sb.append(String.format(" HKL NOT read in (not in internal list?): %d\n", nIgnore));
    sb.append(String.format(" HKL NOT read in (F/sigF cutoff):         %d\n", nCut));
    sb.append(String.format(" HKL in internal list:                    %d\n", reflectionList.hkllist.size()));

    if (logger.isLoggable(Level.INFO)) {
        logger.info(sb.toString());
    }

    if (rFree < 0) {
        refinementData.generateRFree();
    }
    return true;
}

---

From source file:org.fhcrc.cpl.toolbox.filehandler.TabLoader.java

/**
 * Look at first 5 lines of the file and infer col names, data types.
 * Most useful if maps are being returned, otherwise use inferColumnInfo(reader, clazz) to
 * use properties of a bean instead.//from  w w w. java2  s  .c o  m
 *
 * @param reader
 * @throws IOException
 */
private void inferColumnInfo(BufferedReader reader) throws IOException {
    reader.mark(4096 * _scanAheadLineCount);

    String[] lines = new String[_scanAheadLineCount + Math.max(_skipLines, 0)];
    int i;
    for (i = 0; i < lines.length;) {
        String line = reader.readLine();
        if (null == line)
            break;
        if (line.length() == 0 || line.charAt(0) == '#')
            continue;
        lines[i++] = line;
    }
    int nLines = i;
    reader.reset();
    if (nLines == 0) {
        _columns = new ColumnDescriptor[0];
        return;
    }

    int nCols = 0;
    String[][] lineFields = new String[nLines][];
    for (i = 0; i < nLines; i++) {
        lineFields[i] = parseLine(lines[i]);
        nCols = Math.max(nCols, lineFields[i].length);
    }

    ColumnDescriptor[] colDescs = new ColumnDescriptor[nCols];
    for (i = 0; i < nCols; i++)
        colDescs[i] = new ColumnDescriptor();

    //Try to infer types
    int inferStartLine = _skipLines == -1 ? 1 : _skipLines;
    for (int f = 0; f < nCols; f++) {
        int classIndex = -1;
        for (int line = inferStartLine; line < nLines; line++) {
            if (f >= lineFields[line].length)
                continue;
            String field = lineFields[line][f];
            if ("".equals(field))
                continue;

            for (int c = Math.max(classIndex, 0); c < convertClasses.length; c++) {
                //noinspection EmptyCatchBlock
                try {
                    Object o = ConvertUtils.convert(field, convertClasses[c]);
                    //We found a type that works. If it is more general than
                    //what we had before, we must use it.
                    if (o != null && c > classIndex)
                        classIndex = c;
                    break;
                } catch (Exception x) {
                }
            }
        }
        colDescs[f].clazz = classIndex == -1 ? String.class : convertClasses[classIndex];
    }

    //If first line is compatible type for all fields, AND all fields not Strings (dhmay adding 20100502)
    // then there is no header row
    if (_skipLines == -1) {
        boolean firstLineCompat = true;
        boolean allStrings = true;
        String[] fields = lineFields[0];
        for (int f = 0; f < nCols; f++) {
            if ("".equals(fields[f]))
                continue;
            if (colDescs[f].clazz.equals(Integer.TYPE) || colDescs[f].clazz.equals(Double.TYPE)
                    || colDescs[f].clazz.equals(Float.TYPE))
                allStrings = false;
            try {
                Object o = ConvertUtils.convert(fields[f], colDescs[f].clazz);
                if (null == o) {
                    firstLineCompat = false;
                    break;
                }
            } catch (Exception x) {
                firstLineCompat = false;
                break;
            }
        }
        if (firstLineCompat && !allStrings)
            _skipLines = 0;
        else
            _skipLines = 1;
    }

    if (_skipLines > 0) {
        String[] headers = lineFields[_skipLines - 1];
        for (int f = 0; f < nCols; f++)
            colDescs[f].name = (f >= headers.length || "".equals(headers[f])) ? "column" + f : headers[f];
    } else {
        for (int f = 0; f < colDescs.length; f++) {
            ColumnDescriptor colDesc = colDescs[f];
            colDesc.name = "column" + f;
        }
    }

    _columns = colDescs;
}

---

From source file:org.apache.jmeter.services.FileServer.java

private BufferedReader getReader(String alias, boolean recycle, boolean firstLineIsNames) throws IOException {
    FileEntry fileEntry = files.get(alias);
    if (fileEntry != null) {
        BufferedReader reader;
        if (fileEntry.inputOutputObject == null) {
            reader = createBufferedReader(fileEntry);
            fileEntry.inputOutputObject = reader;
            if (firstLineIsNames) {
                // read first line and forget
                reader.readLine();/* w w w  .  jav a  2  s .c  o  m*/
            }
        } else if (!(fileEntry.inputOutputObject instanceof Reader)) {
            throw new IOException("File " + alias + " already in use");
        } else {
            reader = (BufferedReader) fileEntry.inputOutputObject;
            if (recycle) { // need to check if we are at EOF already
                reader.mark(1);
                int peek = reader.read();
                if (peek == -1) { // already at EOF
                    reader.close();
                    reader = createBufferedReader(fileEntry);
                    fileEntry.inputOutputObject = reader;
                    if (firstLineIsNames) {
                        // read first line and forget
                        reader.readLine();
                    }
                } else { // OK, we still have some data, restore it
                    reader.reset();
                }
            }
        }
        return reader;
    } else {
        throw new IOException("File never reserved: " + alias);
    }
}

---

From source file:com.pironet.tda.SunJDKParser.java

/**
 * parses a loggc file stream and reads any found class histograms and adds the to the dump store
 *
 * @param loggcFileStream the stream to read
 * @param root            the root node of the dumps.
 *///from   w  w w  .j av a  2s . c  o m
public void parseLoggcFile(InputStream loggcFileStream, DefaultMutableTreeNode root) {
    final BufferedReader bis = new BufferedReader(new InputStreamReader(loggcFileStream));
    final List<HistogramTableModel> histograms = new Vector<>();
    try {
        while (bis.ready()) {
            bis.mark(getMarkSize());
            String nextLine = bis.readLine();
            if (nextLine.startsWith("num   #instances    #bytes  class name")) {
                bis.reset();
                histograms.add(parseNextClassHistogram(bis));
            }
        }

        // now add the found histograms to the tree.
        for (int i = histograms.size() - 1; i >= 0; i--) {
            DefaultMutableTreeNode dump = getNextDumpForHistogram(root);
            if (dump != null) {
                addHistogramToDump(dump, histograms.get(i));
            }
        }
    } catch (IOException ex) {
        ex.printStackTrace();
    } finally {
        IOUtils.closeQuietly(bis);
    }
}

---

From source file:edu.ucla.stat.SOCR.chart.ChartTree_dynamic.java

/**
 * Creates the tree node and its subnods
 * /*from  www .j a  va2  s  .  c om*/
 * @return A populated tree node.
 */
private MutableTreeNode createChartsNode(String name) {
    //System.out.println("adding-"+name+"-");

    BufferedReader rder = startReaderBuffer();

    DefaultMutableTreeNode node_root = new DefaultMutableTreeNode(name);
    String line, className, chartName;
    StringBuffer sb = new StringBuffer();

    while ((line = readLine(rder)) != null) {
        if (line.toLowerCase().equalsIgnoreCase("[" + name + "]")) {
            while ((line = readLine(rder)) != null) {

                if (line.toLowerCase().startsWith("item")) {
                    line = line.substring(line.indexOf("=") + 1);
                    StringTokenizer tk = new StringTokenizer(line, "=,; ");

                    chartName = tk.nextToken().trim();
                    className = tk.nextToken().trim();
                    //   System.out.println("className =["+className+"]");
                    DefaultMutableTreeNode n = new DefaultMutableTreeNode(
                            new DemoDescription(className, chartName));
                    node_root.add(n);
                } //item

                else if (line.toLowerCase().startsWith("subcategory")) {
                    line = line.substring(line.indexOf("=") + 1);
                    try {
                        rder.mark(100);
                        node_root.add(createChartsNode(line.trim()));
                        rder.reset();
                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                } //subCategory

                else if (line.toLowerCase().startsWith("[")) {
                    //System.out.println("end of "+name);
                    return node_root;
                }

            }
        }

    }
    return node_root;
}

---

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