-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0\r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
+/*\r
+ * Copyright (c) 2009 Peter Troshin JAva Bioinformatics Analysis Web Services\r
+ * (JABAWS) @version: 1.0 This library is free software; you can redistribute it\r
+ * and/or modify it under the terms of the Apache License version 2 as published\r
+ * by the Apache Software Foundation This library is distributed in the hope\r
+ * that it will be useful, but WITHOUT ANY WARRANTY; without even the implied\r
+ * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * Apache License for more details. A copy of the license is in\r
+ * apache_license.txt. It is also available here:\r
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt Any republication or\r
+ * derived work distributed in source code form must include this copyright and\r
+ * license notice.\r
*/\r
\r
package compbio.data.sequence;\r
@Immutable\r
public class FastaSequence {\r
\r
- /**\r
- * Sequence id\r
- */\r
- private String id;\r
-\r
- // TODO what about gapped sequence here! should be indicated\r
- /**\r
- * Returns the string representation of sequence\r
- */\r
- private String sequence;\r
-\r
- private FastaSequence() {\r
- // Default constructor for JaxB\r
- }\r
-\r
- /**\r
- * Upon construction the any whitespace characters are removed from the\r
- * sequence\r
- * \r
- * @param id\r
- * @param sequence\r
- */\r
- public FastaSequence(String id, String sequence) {\r
- this.id = id;\r
- this.sequence = SequenceUtil.cleanSequence(sequence);\r
- }\r
-\r
- /**\r
- * Gets the value of id\r
- * \r
- * @return the value of id\r
- */\r
- public String getId() {\r
- return this.id;\r
- }\r
-\r
- /**\r
- * Gets the value of sequence\r
- * \r
- * @return the value of sequence\r
- */\r
- public String getSequence() {\r
- return this.sequence;\r
- }\r
-\r
- public static int countMatchesInSequence(final String theString,\r
- final String theRegExp) {\r
- final Pattern p = Pattern.compile(theRegExp);\r
- final Matcher m = p.matcher(theString);\r
- int cnt = 0;\r
- while (m.find()) {\r
- cnt++;\r
+ /**\r
+ * Sequence id\r
+ */\r
+ private String id;\r
+\r
+ // TODO what about gapped sequence here! should be indicated\r
+ /**\r
+ * Returns the string representation of sequence\r
+ */\r
+ private String sequence;\r
+\r
+ private FastaSequence() {\r
+ // Default constructor for JaxB\r
}\r
- return cnt;\r
- }\r
-\r
- public String getFormattedFasta() {\r
- return getFormatedSequence(80);\r
- }\r
-\r
- /**\r
- * \r
- * @return one line name, next line sequence, no matter what the sequence\r
- * length is\r
- */\r
- public String getOnelineFasta() {\r
- String fasta = ">" + getId() + SysPrefs.newlinechar;\r
- fasta += getSequence() + SysPrefs.newlinechar;\r
- return fasta;\r
- }\r
-\r
- /**\r
- * Format sequence per width letter in one string. Without spaces.\r
- * \r
- * @return multiple line formated sequence, one line width letters length\r
- * \r
- */\r
- public String getFormatedSequence(final int width) {\r
- if (sequence == null) {\r
- return "";\r
+\r
+ /**\r
+ * Upon construction the any whitespace characters are removed from the\r
+ * sequence\r
+ * \r
+ * @param id\r
+ * @param sequence\r
+ */\r
+ public FastaSequence(String id, String sequence) {\r
+ this.id = id;\r
+ this.sequence = SequenceUtil.cleanSequence(sequence);\r
}\r
\r
- assert width >= 0 : "Wrong width parameter ";\r
-\r
- final StringBuilder sb = new StringBuilder(sequence);\r
- int nchunks = sequence.length() / width;\r
- // add up inserted new line chars\r
- nchunks = (nchunks + sequence.length()) / width;\r
- int nlineCharcounter = 0;\r
- for (int i = 1; i <= nchunks; i++) {\r
- int insPos = width * i + nlineCharcounter;\r
- // to prevent inserting new line in the very end of a sequence then\r
- // it would have failed.\r
- // Also covers the case when the sequences shorter than width\r
- if (sb.length() <= insPos) {\r
- break;\r
- }\r
- sb.insert(insPos, "\n");\r
- nlineCharcounter++;\r
+ /**\r
+ * Gets the value of id\r
+ * \r
+ * @return the value of id\r
+ */\r
+ public String getId() {\r
+ return this.id;\r
}\r
- return sb.toString();\r
- }\r
-\r
- /**\r
- * \r
- * @return sequence length\r
- */\r
- public int getLength() {\r
- return this.sequence.length();\r
- }\r
-\r
- /**\r
- * Same as oneLineFasta\r
- */\r
- @Override\r
- public String toString() {\r
- return this.getOnelineFasta();\r
- }\r
-\r
- @Override\r
- public int hashCode() {\r
- final int prime = 17;\r
- int result = 1;\r
- result = prime * result + ((id == null) ? 0 : id.hashCode());\r
- result = prime * result\r
- + ((sequence == null) ? 0 : sequence.hashCode());\r
- return result;\r
- }\r
-\r
- @Override\r
- public boolean equals(Object obj) {\r
- if (obj == null) {\r
- return false;\r
+\r
+ /**\r
+ * Gets the value of sequence\r
+ * \r
+ * @return the value of sequence\r
+ */\r
+ public String getSequence() {\r
+ return this.sequence;\r
}\r
- if (!(obj instanceof FastaSequence)) {\r
- return false;\r
+\r
+ public static int countMatchesInSequence(final String theString,\r
+ final String theRegExp) {\r
+ final Pattern p = Pattern.compile(theRegExp);\r
+ final Matcher m = p.matcher(theString);\r
+ int cnt = 0;\r
+ while (m.find()) {\r
+ cnt++;\r
+ }\r
+ return cnt;\r
}\r
- FastaSequence fs = (FastaSequence) obj;\r
- if (!fs.getId().equals(this.getId())) {\r
- return false;\r
+\r
+ public String getFormattedFasta() {\r
+ return getFormatedSequence(80);\r
}\r
- if (!fs.getSequence().equalsIgnoreCase(this.getSequence())) {\r
- return false;\r
+\r
+ /**\r
+ * \r
+ * @return one line name, next line sequence, no matter what the sequence\r
+ * length is\r
+ */\r
+ public String getOnelineFasta() {\r
+ String fasta = ">" + getId() + SysPrefs.newlinechar;\r
+ fasta += getSequence() + SysPrefs.newlinechar;\r
+ return fasta;\r
+ }\r
+\r
+ /**\r
+ * Format sequence per width letter in one string. Without spaces.\r
+ * \r
+ * @return multiple line formated sequence, one line width letters length\r
+ * \r
+ */\r
+ public String getFormatedSequence(final int width) {\r
+ if (sequence == null) {\r
+ return "";\r
+ }\r
+\r
+ assert width >= 0 : "Wrong width parameter ";\r
+\r
+ final StringBuilder sb = new StringBuilder(sequence);\r
+ // int tail = nrOfWindows % WIN_SIZE;\r
+ // final int turns = (nrOfWindows - tail) / WIN_SIZE;\r
+\r
+ int tailLen = sequence.length() % width;\r
+ // add up inserted new line chars\r
+ int nchunks = (sequence.length() - tailLen) / width;\r
+ int nlineCharcounter = 0;\r
+ int insPos = 0;\r
+ for (int i = 1; i <= nchunks; i++) {\r
+ insPos = width * i + nlineCharcounter;\r
+ // to prevent inserting new line in the very end of a sequence then\r
+ // it would have failed.\r
+ if (sb.length() <= insPos) {\r
+ break;\r
+ }\r
+ sb.insert(insPos, "\n");\r
+ nlineCharcounter++;\r
+ }\r
+ // sb.insert(insPos + tailLen, "\n");\r
+ return sb.toString();\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return sequence length\r
+ */\r
+ public int getLength() {\r
+ return this.sequence.length();\r
+ }\r
+\r
+ /**\r
+ * Same as oneLineFasta\r
+ */\r
+ @Override\r
+ public String toString() {\r
+ return this.getOnelineFasta();\r
+ }\r
+\r
+ @Override\r
+ public int hashCode() {\r
+ final int prime = 17;\r
+ int result = 1;\r
+ result = prime * result + ((id == null) ? 0 : id.hashCode());\r
+ result = prime * result\r
+ + ((sequence == null) ? 0 : sequence.hashCode());\r
+ return result;\r
+ }\r
+\r
+ @Override\r
+ public boolean equals(Object obj) {\r
+ if (obj == null) {\r
+ return false;\r
+ }\r
+ if (!(obj instanceof FastaSequence)) {\r
+ return false;\r
+ }\r
+ FastaSequence fs = (FastaSequence) obj;\r
+ if (!fs.getId().equals(this.getId())) {\r
+ return false;\r
+ }\r
+ if (!fs.getSequence().equalsIgnoreCase(this.getSequence())) {\r
+ return false;\r
+ }\r
+ return true;\r
}\r
- return true;\r
- }\r
\r
}\r
git://source.jalview.org / jabaws.git / blobdiff