import java.util.*;\r
\r
\r
-public class FastaFile extends AlignFile {\r
- public FastaFile() {\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class FastaFile extends AlignFile\r
+{\r
+ /**\r
+ * Creates a new FastaFile object.\r
+ */\r
+ public FastaFile()\r
+ {\r
}\r
\r
- public FastaFile(String inStr) {\r
+ /**\r
+ * Creates a new FastaFile object.\r
+ *\r
+ * @param inStr DOCUMENT ME!\r
+ */\r
+ public FastaFile(String inStr)\r
+ {\r
super(inStr);\r
}\r
\r
- public FastaFile(String inFile, String type) throws IOException {\r
+ /**\r
+ * Creates a new FastaFile object.\r
+ *\r
+ * @param inFile DOCUMENT ME!\r
+ * @param type DOCUMENT ME!\r
+ *\r
+ * @throws IOException DOCUMENT ME!\r
+ */\r
+ public FastaFile(String inFile, String type) throws IOException\r
+ {\r
super(inFile, type);\r
}\r
\r
- public void parse() throws IOException {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @throws IOException DOCUMENT ME!\r
+ */\r
+ public void parse() throws IOException\r
+ {\r
String id = "";\r
StringBuffer seq = new StringBuffer();\r
int count = 0;\r
\r
String line;\r
\r
- while ((line = nextLine()) != null) {\r
- if (line.length() > 0) {\r
+ while ((line = nextLine()) != null)\r
+ {\r
+ if (line.length() > 0)\r
+ {\r
// Do we have an id line?\r
// JBPNote - this code needs to be standardised to EBI/whatever for the\r
// >dbref/dbref/dbref|refid1|refid2|refid3 'human-readable' style of naming (should it really exist)\r
-\r
- if (line.substring(0, 1).equals(">")) {\r
- if (count != 0) {\r
- if (sstart != 0) {\r
- seqs.addElement(new Sequence(id,\r
- seq.toString(), sstart, send));\r
- } else {\r
- seqs.addElement(new Sequence(id,\r
- seq.toString(), 1,\r
+ if (line.substring(0, 1).equals(">"))\r
+ {\r
+ if (count != 0)\r
+ {\r
+ if (sstart != 0)\r
+ {\r
+ seqs.addElement(new Sequence(id, seq.toString(),\r
+ sstart, send));\r
+ }\r
+ else\r
+ {\r
+ seqs.addElement(new Sequence(id, seq.toString(), 1,\r
seq.length()));\r
}\r
}\r
\r
com.stevesoft.pat.Regex dbId = new com.stevesoft.pat.Regex(\r
"[A-Za-z-]+/?[A-Za-z-]+\\|(\\w+)\\|(.+)");\r
+\r
// JBPNote At the moment - we don't get rid of the friendly names but this\r
// behaviour is probably wrong in the long run.\r
- if (dbId.search(id)) {\r
+ if (dbId.search(id))\r
+ {\r
String dbid = dbId.stringMatched(1);\r
String idname = dbId.stringMatched(2);\r
- if ( (idname.length() > 0) &&\r
- (idname.indexOf("_") > -1)) {\r
- id = idname; // use the friendly name - apparently no dbid\r
- } else\r
- if (dbid.length()>1) {\r
+\r
+ if ((idname.length() > 0) &&\r
+ (idname.indexOf("_") > -1))\r
+ {\r
+ id = idname; // use the friendly name - apparently no dbid\r
+ }\r
+ else if (dbid.length() > 1)\r
+ {\r
id = dbid; // ignore the friendly name - we lose uniprot accession ID otherwise\r
}\r
}\r
\r
- if (id.indexOf("/") > 0) {\r
+ if (id.indexOf("/") > 0)\r
+ {\r
StringTokenizer st = new StringTokenizer(id, "/");\r
\r
- if (st.countTokens() == 2) {\r
+ if (st.countTokens() == 2)\r
+ {\r
id = st.nextToken();\r
\r
String tmp = st.nextToken();\r
\r
st = new StringTokenizer(tmp, "-");\r
\r
- if (st.countTokens() == 2) {\r
+ if (st.countTokens() == 2)\r
+ {\r
sstart = Integer.valueOf(st.nextToken())\r
.intValue();\r
send = Integer.valueOf(st.nextToken()).intValue();\r
}\r
\r
seq = new StringBuffer();\r
- } else {\r
+ }\r
+ else\r
+ {\r
seq = seq.append(line);\r
}\r
}\r
}\r
\r
- if (count > 0) {\r
- if (!isValidProteinSequence(seq.toString().toUpperCase())) {\r
+ if (count > 0)\r
+ {\r
+ if (!isValidProteinSequence(seq.toString().toUpperCase()))\r
+ {\r
throw new IOException("Invalid protein sequence");\r
}\r
\r
- if (sstart != 0) {\r
+ if (sstart != 0)\r
+ {\r
seqs.addElement(new Sequence(id, seq.toString().toUpperCase(),\r
sstart, send));\r
- } else {\r
+ }\r
+ else\r
+ {\r
seqs.addElement(new Sequence(id, seq.toString().toUpperCase(),\r
1, seq.length()));\r
}\r
}\r
}\r
\r
- public static String print(SequenceI[] s) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param s DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static String print(SequenceI[] s)\r
+ {\r
return print(s, 72);\r
}\r
\r
- public static String print(SequenceI[] s, int len) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param s DOCUMENT ME!\r
+ * @param len DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static String print(SequenceI[] s, int len)\r
+ {\r
return print(s, len, true);\r
}\r
\r
- public static String print(SequenceI[] s, int len, boolean gaps) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param s DOCUMENT ME!\r
+ * @param len DOCUMENT ME!\r
+ * @param gaps DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static String print(SequenceI[] s, int len, boolean gaps)\r
+ {\r
return print(s, len, gaps, true);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param s DOCUMENT ME!\r
+ * @param len DOCUMENT ME!\r
+ * @param gaps DOCUMENT ME!\r
+ * @param displayId DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public static String print(SequenceI[] s, int len, boolean gaps,\r
- boolean displayId) {\r
+ boolean displayId)\r
+ {\r
StringBuffer out = new StringBuffer();\r
int i = 0;\r
\r
- while ((i < s.length) && (s[i] != null)) {\r
+ while ((i < s.length) && (s[i] != null))\r
+ {\r
String seq = "";\r
\r
- if (gaps) {\r
+ if (gaps)\r
+ {\r
seq = s[i].getSequence();\r
- } else {\r
+ }\r
+ else\r
+ {\r
seq = AlignSeq.extractGaps("-. ", s[i].getSequence());\r
}\r
\r
\r
int nochunks = (seq.length() / len) + 1;\r
\r
- for (int j = 0; j < nochunks; j++) {\r
+ for (int j = 0; j < nochunks; j++)\r
+ {\r
int start = j * len;\r
int end = start + len;\r
\r
- if (end < seq.length()) {\r
+ if (end < seq.length())\r
+ {\r
out.append(seq.substring(start, end) + "\n");\r
- } else if (start < seq.length()) {\r
+ }\r
+ else if (start < seq.length())\r
+ {\r
out.append(seq.substring(start) + "\n");\r
}\r
}\r
return out.toString();\r
}\r
\r
- public String print() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String print()\r
+ {\r
return print(getSeqsAsArray());\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff