* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.io;\r
\r
-import jalview.datamodel.*;\r
import jalview.analysis.*;\r
\r
+import jalview.datamodel.*;\r
+\r
import java.io.*;\r
+\r
import java.util.*;\r
\r
+\r
public class PIRFile extends AlignFile {\r
+ Vector words = new Vector(); //Stores the words in a line after splitting\r
+\r
+ public PIRFile() {\r
+ }\r
\r
- Vector words = new Vector(); //Stores the words in a line after splitting\r
-\r
- public PIRFile()\r
- {}\r
-\r
- public PIRFile(String inStr) {\r
- super(inStr);\r
- }\r
-\r
- public PIRFile(String inFile, String type) throws IOException {\r
- super(inFile,type);\r
- }\r
-\r
- public void parse() {\r
- try{\r
- String id, start, end;\r
- StringBuffer sequence;\r
- String line = null;\r
- while( (line = nextLine())!=null)\r
- {\r
- try{\r
- id = line.substring(line.indexOf(";") + 1, line.indexOf("/"));\r
- line = line.substring(line.indexOf("/") + 1);\r
- start = line.substring(0, line.indexOf("-"));\r
- end = line.substring(line.indexOf("-") + 1);\r
- }catch(Exception ex)\r
- { id="No id"; start="0"; end="0"; }\r
-\r
- sequence = new StringBuffer();\r
-\r
- line = nextLine(); // this is the title line\r
-\r
- boolean starFound = false;\r
- do\r
- {\r
- line = nextLine();\r
- sequence.append( line );\r
- if(line.indexOf("*")>-1)\r
- starFound = true;\r
-\r
- }while(!starFound);\r
-\r
- sequence.setLength( sequence.length()-1);\r
-\r
- Sequence newSeq = new Sequence(id,\r
- sequence.toString(),\r
- Integer.parseInt(start),\r
- Integer.parseInt(end));\r
- seqs.addElement(newSeq);\r
- }\r
+ public PIRFile(String inStr) {\r
+ super(inStr);\r
+ }\r
\r
+ public PIRFile(String inFile, String type) throws IOException {\r
+ super(inFile, type);\r
}\r
- catch(Exception ex){ex.printStackTrace();}\r
- }\r
-\r
- public String print() {\r
- return print(getSeqsAsArray());\r
- }\r
- public static String print(SequenceI[] s) {\r
- return print(s,72,true);\r
- }\r
- public static String print(SequenceI[] s, int len) {\r
- return print(s,len,true);\r
- }\r
- public static String print(SequenceI[] s, int len,boolean gaps) {\r
- StringBuffer out = new StringBuffer();\r
- int i = 0;\r
-\r
- while (i < s.length && s[i] != null) {\r
- String seq = "";\r
- if (gaps) {\r
- seq = s[i].getSequence() + "*";\r
- } else {\r
- seq = AlignSeq.extractGaps(s[i].getSequence(),"-");\r
- seq = AlignSeq.extractGaps(seq,".");\r
- seq = AlignSeq.extractGaps(seq," ");\r
- seq = seq + "*";\r
- }\r
-\r
- out.append(">P1;" + s[i].getName() + "/" + s[i].getStart()+ "-" + s[i].getEnd() + "\n");\r
- out.append(" Dummy title\n");\r
- int nochunks = seq.length() / len + 1;\r
-\r
- for (int j = 0; j < nochunks; j++) {\r
- int start = j*len;\r
- int end = start + len;\r
-\r
- if (end < seq.length()) {\r
- out.append(seq.substring(start,end) + "\n");\r
- } else if (start < seq.length()) {\r
- out.append(seq.substring(start) + "\n");\r
+\r
+ public void parse() {\r
+ try {\r
+ String id;\r
+ String start;\r
+ String end;\r
+ StringBuffer sequence;\r
+ String line = null;\r
+\r
+ while ((line = nextLine()) != null) {\r
+ try {\r
+ id = line.substring(line.indexOf(";") + 1, line.indexOf("/"));\r
+ line = line.substring(line.indexOf("/") + 1);\r
+ start = line.substring(0, line.indexOf("-"));\r
+ end = line.substring(line.indexOf("-") + 1);\r
+ } catch (Exception ex) {\r
+ id = "No id";\r
+ start = "0";\r
+ end = "0";\r
+ }\r
+\r
+ sequence = new StringBuffer();\r
+\r
+ line = nextLine(); // this is the title line\r
+\r
+ boolean starFound = false;\r
+\r
+ do {\r
+ line = nextLine();\r
+ sequence.append(line);\r
+\r
+ if (line.indexOf("*") > -1) {\r
+ starFound = true;\r
+ }\r
+ } while (!starFound);\r
+\r
+ sequence.setLength(sequence.length() - 1);\r
+\r
+ Sequence newSeq = new Sequence(id, sequence.toString(),\r
+ Integer.parseInt(start), Integer.parseInt(end));\r
+ seqs.addElement(newSeq);\r
+ }\r
+ } catch (Exception ex) {\r
+ ex.printStackTrace();\r
}\r
- }\r
- i++;\r
}\r
- return out.toString();\r
- }\r
\r
- public static void main(String[] args) {\r
- String inStr = ">P1;LCAT_MOUSE_90.35\nMGLPGSPWQRVLLLLGLLLPPATPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNRLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDFNLFLPLGVDCWIDNTRIVYNHSSGRVSNAPGVQIRVPGFGKTESVEYVDDNKLAGY\n\n>LCAT_PAPAN_95.78\nMGPPGSPWQWVPLLLGLLLPPAAPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNQLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDLNMFLPLGVDCWIDNTRVVYNRSSGLVSNAPGVQIRVPGFGKTYSVEYLDSSKLAGY\nLHTLVQNLVNNGYVRDETVRAAPYDWRLEPGQQEEYYHKLAGLVEEMHAAYGKPVFLIGHSLGCLHLLYFLL\n";\r
- PIRFile fa = new PIRFile(inStr);\r
- }\r
-}\r
+ public String print() {\r
+ return print(getSeqsAsArray());\r
+ }\r
\r
+ public static String print(SequenceI[] s) {\r
+ return print(s, 72, true);\r
+ }\r
\r
+ public static String print(SequenceI[] s, int len) {\r
+ return print(s, len, true);\r
+ }\r
\r
+ public static String print(SequenceI[] s, int len, boolean gaps) {\r
+ StringBuffer out = new StringBuffer();\r
+ int i = 0;\r
+\r
+ while ((i < s.length) && (s[i] != null)) {\r
+ String seq = "";\r
+\r
+ if (gaps) {\r
+ seq = s[i].getSequence() + "*";\r
+ } else {\r
+ seq = AlignSeq.extractGaps(s[i].getSequence(), "-");\r
+ seq = AlignSeq.extractGaps(seq, ".");\r
+ seq = AlignSeq.extractGaps(seq, " ");\r
+ seq = seq + "*";\r
+ }\r
+\r
+ out.append(">P1;" + s[i].getName() + "/" + s[i].getStart() + "-" +\r
+ s[i].getEnd() + "\n");\r
+ out.append(" Dummy title\n");\r
+\r
+ int nochunks = (seq.length() / len) + 1;\r
+\r
+ for (int j = 0; j < nochunks; j++) {\r
+ int start = j * len;\r
+ int end = start + len;\r
+\r
+ if (end < seq.length()) {\r
+ out.append(seq.substring(start, end) + "\n");\r
+ } else if (start < seq.length()) {\r
+ out.append(seq.substring(start) + "\n");\r
+ }\r
+ }\r
+\r
+ i++;\r
+ }\r
+\r
+ return out.toString();\r
+ }\r
+\r
+ public static void main(String[] args) {\r
+ String inStr = ">P1;LCAT_MOUSE_90.35\nMGLPGSPWQRVLLLLGLLLPPATPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNRLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDFNLFLPLGVDCWIDNTRIVYNHSSGRVSNAPGVQIRVPGFGKTESVEYVDDNKLAGY\n\n>LCAT_PAPAN_95.78\nMGPPGSPWQWVPLLLGLLLPPAAPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNQLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDLNMFLPLGVDCWIDNTRVVYNRSSGLVSNAPGVQIRVPGFGKTYSVEYLDSSKLAGY\nLHTLVQNLVNNGYVRDETVRAAPYDWRLEPGQQEEYYHKLAGLVEEMHAAYGKPVFLIGHSLGCLHLLYFLL\n";\r
+ PIRFile fa = new PIRFile(inStr);\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / blobdiff