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package jalview.io; |
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import jalview.datamodel.Sequence; |
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import jalview.datamodel.SequenceI; |
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import jalview.util.Comparison; |
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import jalview.util.Format; |
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import java.io.IOException; |
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import java.util.ArrayList; |
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import java.util.Hashtable; |
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import java.util.List; |
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import java.util.StringTokenizer; |
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@author |
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@version |
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| 89.7% |
Uncovered Elements: 22 (213) |
Complexity: 49 |
Complexity Density: 0.36 |
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public class MSFfile extends AlignFile |
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{ |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
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2 |
public MSFfile()... |
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{ |
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} |
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@param |
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@param |
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@throws |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public MSFfile(String inFile, DataSourceType type) throws IOException... |
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{ |
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super(inFile, type); |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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2 |
public MSFfile(FileParse source) throws IOException... |
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{ |
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super(source); |
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} |
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| 89.8% |
Uncovered Elements: 6 (59) |
Complexity: 13 |
Complexity Density: 0.33 |
|
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2 |
@Override... |
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public void parse() throws IOException |
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{ |
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boolean seqFlag = false; |
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List<String> headers = new ArrayList<String>(); |
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Hashtable<String, StringBuilder> seqhash = new Hashtable<String, StringBuilder>(); |
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try |
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{ |
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String line; |
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while ((line = nextLine()) != null) |
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{ |
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StringTokenizer str = new StringTokenizer(line); |
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String key = null; |
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while (str.hasMoreTokens()) |
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{ |
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String inStr = str.nextToken(); |
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if (inStr.indexOf("Name:") != -1) |
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{ |
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key = str.nextToken(); |
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headers.add(key); |
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} |
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if (inStr.indexOf("//") != -1) |
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{ |
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seqFlag = true; |
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} |
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if ((inStr.indexOf("//") == -1) && seqFlag) |
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{ |
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key = inStr; |
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StringBuilder tempseq; |
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if (seqhash.containsKey(key)) |
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{ |
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tempseq = seqhash.get(key); |
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} |
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else |
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{ |
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tempseq = new StringBuilder(64); |
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seqhash.put(key, tempseq); |
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} |
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while (str.hasMoreTokens()) |
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{ |
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String sequenceBlock = str.nextToken(); |
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tempseq.append(sequenceBlock); |
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} |
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} |
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} |
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} |
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} catch (IOException e) |
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{ |
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System.err.println("Exception parsing MSFFile " + e); |
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e.printStackTrace(); |
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} |
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this.noSeqs = headers.size(); |
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for (int i = 0; i < headers.size(); i++) |
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{ |
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if (seqhash.get(headers.get(i)) != null) |
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{ |
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String head = headers.get(i); |
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String seq = seqhash.get(head).toString(); |
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if (maxLength < head.length()) |
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{ |
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maxLength = head.length(); |
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} |
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seq = seq.replace('~', '.'); |
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Sequence newSeq = parseId(head); |
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newSeq.setSequence(seq); |
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seqs.addElement(newSeq); |
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} |
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else |
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{ |
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System.err.println("MSFFile Parser: Can't find sequence for " |
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+ headers.get(i)); |
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} |
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} |
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} |
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@param |
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@return |
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| 78.6% |
Uncovered Elements: 3 (14) |
Complexity: 4 |
Complexity Density: 0.4 |
|
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30 |
public int checkSum(String seq)... |
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{ |
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int check = 0; |
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String sequence = seq.toUpperCase(); |
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for (int i = 0; i < sequence.length(); i++) |
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{ |
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try |
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{ |
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int value = sequence.charAt(i); |
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if (value != -1) |
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{ |
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check += (i % 57 + 1) * value; |
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} |
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} catch (Exception e) |
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{ |
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System.err.println("Exception during MSF Checksum calculation"); |
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e.printStackTrace(); |
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} |
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} |
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return check % 10000; |
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} |
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@param |
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@param |
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@return |
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| 91.7% |
Uncovered Elements: 11 (132) |
Complexity: 29 |
Complexity Density: 0.34 |
|
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1 |
@Override... |
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public String print(SequenceI[] sqs, boolean jvSuffix) |
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{ |
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boolean is_NA = Comparison.isNucleotide(sqs); |
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SequenceI[] s = new SequenceI[sqs.length]; |
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StringBuilder out = new StringBuilder(256); |
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out.append("!!").append(is_NA ? "NA" : "AA") |
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.append("_MULTIPLE_ALIGNMENT 1.0"); |
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out.append(newline); |
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out.append(newline); |
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int max = 0; |
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int maxid = 0; |
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int i = 0; |
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while ((i < sqs.length) && (sqs[i] != null)) |
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{ |
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String seqString = sqs[i].getSequenceAsString().replace('-', '.'); |
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StringBuilder sb = new StringBuilder(seqString); |
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for (int ii = 0; ii < sb.length(); ii++) |
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{ |
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if (sb.charAt(ii) == '.') |
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{ |
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sb.setCharAt(ii, '~'); |
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} |
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else |
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{ |
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break; |
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} |
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} |
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for (int ii = sb.length() - 1; ii > 0; ii--) |
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{ |
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if (sb.charAt(ii) == '.') |
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{ |
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sb.setCharAt(ii, '~'); |
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} |
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else |
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{ |
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break; |
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} |
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} |
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s[i] = new Sequence(sqs[i].getName(), sb.toString(), |
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sqs[i].getStart(), sqs[i].getEnd()); |
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if (sb.length() > max) |
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{ |
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max = sb.length(); |
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} |
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i++; |
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} |
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1 |
Format maxLenpad = new Format( |
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"%" + (new String("" + max)).length() + "d"); |
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1 |
Format maxChkpad = new Format( |
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"%" + (new String("1" + max)).length() + "d"); |
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1 |
i = 0; |
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1 |
int bigChecksum = 0; |
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1 |
int[] checksums = new int[s.length]; |
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while (i < s.length) |
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{ |
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checksums[i] = checkSum(s[i].getSequenceAsString()); |
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bigChecksum += checksums[i]; |
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i++; |
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} |
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1 |
long maxNB = 0; |
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out.append(" MSF: " + s[0].getLength() + " Type: " |
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+ (is_NA ? "N" : "P") + " Check: " + (bigChecksum % 10000) |
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+ " .."); |
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out.append(newline); |
301 |
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out.append(newline); |
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out.append(newline); |
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1 |
String[] nameBlock = new String[s.length]; |
305 |
1 |
String[] idBlock = new String[s.length]; |
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1 |
i = 0; |
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while ((i < s.length) && (s[i] != null)) |
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{ |
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nameBlock[i] = new String(" Name: " + printId(s[i], jvSuffix) + " "); |
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idBlock[i] = new String("Len: " + maxLenpad.form(s[i].getLength()) |
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+ " Check: " + maxChkpad.form(checksums[i]) |
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+ " Weight: 1.00" + newline); |
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317 |
15 |
if (s[i].getName().length() > maxid) |
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{ |
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3 |
maxid = s[i].getName().length(); |
320 |
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} |
321 |
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322 |
15 |
if (nameBlock[i].length() > maxNB) |
323 |
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{ |
324 |
3 |
maxNB = nameBlock[i].length(); |
325 |
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} |
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15 |
i++; |
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} |
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330 |
1 |
if (maxid < 10) |
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{ |
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maxid = 10; |
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} |
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335 |
1 |
if (maxNB < 15) |
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{ |
337 |
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maxNB = 15; |
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} |
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340 |
1 |
Format nbFormat = new Format("%-" + maxNB + "s"); |
341 |
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342 |
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for (i = 0; (i < s.length) && (s[i] != null); i++) |
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{ |
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out.append(nbFormat.form(nameBlock[i]) + idBlock[i]); |
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} |
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maxid++; |
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out.append(newline); |
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1 |
out.append(newline); |
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out.append("//"); |
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1 |
out.append(newline); |
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1 |
out.append(newline); |
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1 |
int len = 50; |
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1 |
int nochunks = (max / len) + (max % len > 0 ? 1 : 0); |
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357 |
5 |
for (i = 0; i < nochunks; i++) |
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{ |
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4 |
int j = 0; |
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361 |
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while ((j < s.length) && (s[j] != null)) |
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{ |
363 |
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String name = printId(s[j], jvSuffix); |
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out.append(new Format("%-" + maxid + "s").form(name + " ")); |
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367 |
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for (int k = 0; k < 5; k++) |
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{ |
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300 |
int start = (i * 50) + (k * 10); |
370 |
300 |
int end = start + 10; |
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|
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300 |
int length = s[j].getLength(); |
373 |
300 |
if ((end < length) |
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&& (start < length)) |
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{ |
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out.append(s[j].getSequence(start, end)); |
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if (k < 4) |
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{ |
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out.append(" "); |
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} |
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else |
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{ |
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out.append(newline); |
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} |
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} |
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else |
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{ |
389 |
75 |
if (start < length) |
390 |
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{ |
391 |
15 |
out.append(s[j].getSequenceAsString().substring(start)); |
392 |
15 |
out.append(newline); |
393 |
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} |
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else |
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{ |
396 |
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if (k == 0) |
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{ |
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out.append(newline); |
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} |
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} |
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} |
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} |
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60 |
j++; |
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} |
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407 |
4 |
out.append(newline); |
408 |
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} |
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1 |
return out.toString(); |
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} |
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} |