import java.util.*;\r
\r
\r
-public class SequenceFeatureFetcher implements Runnable {\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class SequenceFeatureFetcher implements Runnable\r
+{\r
AlignmentI align;\r
AlignmentPanel ap;\r
ArrayList unknownSequences;\r
CutAndPasteTransfer output = new CutAndPasteTransfer();\r
StringBuffer sbuffer = new StringBuffer();\r
\r
- public SequenceFeatureFetcher(AlignmentI align, AlignmentPanel ap) {\r
+ /**\r
+ * Creates a new SequenceFeatureFetcher object.\r
+ *\r
+ * @param align DOCUMENT ME!\r
+ * @param ap DOCUMENT ME!\r
+ */\r
+ public SequenceFeatureFetcher(AlignmentI align, AlignmentPanel ap)\r
+ {\r
unknownSequences = new ArrayList();\r
this.align = align;\r
this.ap = ap;\r
thread.start();\r
}\r
\r
- public void run() {\r
-\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void run()\r
+ {\r
RandomAccessFile out = null;\r
\r
- try {\r
- String cache = System.getProperty("user.home") + "/.jalview.uniprot.xml";\r
+ try\r
+ {\r
+ String cache = System.getProperty("user.home") +\r
+ "/.jalview.uniprot.xml";\r
\r
File test = new File(cache);\r
\r
- if (!test.exists()) {\r
+ if (!test.exists())\r
+ {\r
out = new RandomAccessFile(cache, "rw");\r
out.writeBytes("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");\r
out.writeBytes("<UNIPROT_CACHE>\n");\r
- } else {\r
+ }\r
+ else\r
+ {\r
out = new RandomAccessFile(cache, "rw");\r
\r
// open exisiting cache and remove </UNIPROT_CACHE> from the end\r
long lastLine = 0;\r
String data;\r
\r
- while ((data = out.readLine()) != null) {\r
- if (data.indexOf("</entry>") > -1) {\r
+ while ((data = out.readLine()) != null)\r
+ {\r
+ if (data.indexOf("</entry>") > -1)\r
+ {\r
lastLine = out.getFilePointer();\r
}\r
}\r
int seqIndex = 0;\r
Vector sequences = align.getSequences();\r
\r
- while (seqIndex < sequences.size()) {\r
+ while (seqIndex < sequences.size())\r
+ {\r
ArrayList ids = new ArrayList();\r
\r
for (int i = 0; (seqIndex < sequences.size()) && (i < 50);\r
- seqIndex++, i++) {\r
+ seqIndex++, i++)\r
+ {\r
SequenceI sequence = (SequenceI) sequences.get(seqIndex);\r
ids.add(sequence.getName());\r
}\r
\r
tryLocalCacheFirst(ids, align);\r
\r
- if (ids.size() > 0) {\r
+ if (ids.size() > 0)\r
+ {\r
StringBuffer remainingIds = new StringBuffer("uniprot:");\r
\r
for (int i = 0; i < ids.size(); i++)\r
String[] result = ebi.fetchData(remainingIds.toString(),\r
"xml", null);\r
\r
- if (result != null) {\r
+ if (result != null)\r
+ {\r
ReadUniprotFile(result, out, align);\r
}\r
}\r
}\r
\r
- if (out != null) {\r
+ if (out != null)\r
+ {\r
out.writeBytes("</UNIPROT_CACHE>\n");\r
out.close();\r
}\r
- } catch (Exception ex) {\r
+ }\r
+ catch (Exception ex)\r
+ {\r
ex.printStackTrace();\r
}\r
\r
findMissingIds(align);\r
\r
- if (sbuffer.length() > 0) {\r
+ if (sbuffer.length() > 0)\r
+ {\r
output.setText(\r
"Your sequences have been matched to Uniprot. Some of the ids have been\n" +\r
"altered, most likely the start/end residue will have been updated.\n" +\r
Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);\r
}\r
\r
- if (unknownSequences.size() > 0) {\r
+ if (unknownSequences.size() > 0)\r
+ {\r
//ignore for now!!!!!!!!!!\r
// WSWUBlastClient blastClient = new WSWUBlastClient(align, unknownSequences);\r
}\r
jalview.gui.PaintRefresher.Refresh(null, align);\r
}\r
\r
- void ReadUniprotFile(String[] result, RandomAccessFile out, AlignmentI align) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param result DOCUMENT ME!\r
+ * @param out DOCUMENT ME!\r
+ * @param align DOCUMENT ME!\r
+ */\r
+ void ReadUniprotFile(String[] result, RandomAccessFile out, AlignmentI align)\r
+ {\r
SequenceI sequence = null;\r
Vector features = null;\r
String type;\r
String end;\r
String pdb = null;\r
\r
- for (int r = 0; r < result.length; r++) {\r
- if ((sequence == null) && (result[r].indexOf("<name>") > -1)) {\r
+ for (int r = 0; r < result.length; r++)\r
+ {\r
+ if ((sequence == null) && (result[r].indexOf("<name>") > -1))\r
+ {\r
long filePointer = 0;\r
\r
- if (out != null) {\r
- try {\r
+ if (out != null)\r
+ {\r
+ try\r
+ {\r
filePointer = out.getFilePointer();\r
out.writeBytes("<entry>\n");\r
- } catch (Exception ex) {\r
+ }\r
+ catch (Exception ex)\r
+ {\r
}\r
}\r
\r
String seqName = parseElement(result[r], "<name>", out);\r
sequence = align.findName(seqName);\r
\r
- if (sequence == null) {\r
+ if (sequence == null)\r
+ {\r
sequence = align.findName(seqName.substring(0,\r
seqName.indexOf('_')));\r
\r
- if (sequence != null) {\r
+ if (sequence != null)\r
+ {\r
sbuffer.append("changing " + sequence.getName() +\r
" to " + seqName + "\n");\r
sequence.setName(seqName);\r
}\r
}\r
\r
- if (sequence == null) {\r
+ if (sequence == null)\r
+ {\r
sbuffer.append("UNIPROT updated suggestion is " +\r
result[r] + "\n");\r
sequence = align.findName(result[r]);\r
\r
// this entry has been suggested by ebi.\r
// doesn't match id in alignment file\r
- try {\r
+ try\r
+ {\r
out.setLength(filePointer);\r
- } catch (Exception ex) {\r
+ }\r
+ catch (Exception ex)\r
+ {\r
}\r
\r
// now skip to next entry\r
pdb = "";\r
}\r
\r
- if (sequence == null) {\r
+ if (sequence == null)\r
+ {\r
continue;\r
}\r
\r
- if (result[r].indexOf("<property type=\"pdb accession\"") > -1) {\r
+ if (result[r].indexOf("<property type=\"pdb accession\"") > -1)\r
+ {\r
pdb = parseValue(result[r], "value=", out);\r
sequence.setPDBId(pdb);\r
}\r
\r
- if (result[r].indexOf("feature type") > -1) {\r
+ if (result[r].indexOf("feature type") > -1)\r
+ {\r
type = parseValue(result[r], "type=", out);\r
description = parseValue(result[r], "description=", null);\r
status = parseValue(result[r], "status=", null);\r
\r
- while (result[r].indexOf("position") == -1) {\r
+ while (result[r].indexOf("position") == -1)\r
+ {\r
r++; //<location>\r
}\r
\r
// r++;\r
- if (result[r].indexOf("begin") > -1) {\r
+ if (result[r].indexOf("begin") > -1)\r
+ {\r
start = parseValue(result[r], "position=", out);\r
end = parseValue(result[++r], "position=", out);\r
- } else {\r
+ }\r
+ else\r
+ {\r
start = parseValue(result[r], "position=", out);\r
end = parseValue(result[r], "position=", null);\r
}\r
int sstart = Integer.parseInt(start);\r
int eend = Integer.parseInt(end);\r
\r
- if (out != null) {\r
- try {\r
+ if (out != null)\r
+ {\r
+ try\r
+ {\r
out.writeBytes("</feature>\n");\r
- } catch (Exception ex) {\r
+ }\r
+ catch (Exception ex)\r
+ {\r
}\r
}\r
\r
features.add(sf);\r
}\r
\r
- if (result[r].indexOf("<sequence") > -1) {\r
+ if (result[r].indexOf("<sequence") > -1)\r
+ {\r
StringBuffer seqString = new StringBuffer();\r
\r
- if (out != null) {\r
- try {\r
+ if (out != null)\r
+ {\r
+ try\r
+ {\r
out.writeBytes(result[r] + "\n");\r
- } catch (Exception ex) {\r
+ }\r
+ catch (Exception ex)\r
+ {\r
}\r
}\r
\r
- while (result[++r].indexOf("</sequence>") == -1) {\r
+ while (result[++r].indexOf("</sequence>") == -1)\r
+ {\r
seqString.append(result[r]);\r
\r
- if (out != null) {\r
- try {\r
+ if (out != null)\r
+ {\r
+ try\r
+ {\r
out.writeBytes(result[r] + "\n");\r
- } catch (Exception ex) {\r
+ }\r
+ catch (Exception ex)\r
+ {\r
}\r
}\r
}\r
\r
- if (out != null) {\r
- try {\r
+ if (out != null)\r
+ {\r
+ try\r
+ {\r
out.writeBytes(result[r] + "\n");\r
- } catch (Exception ex) {\r
+ }\r
+ catch (Exception ex)\r
+ {\r
}\r
}\r
\r
StringBuffer nonGapped = new StringBuffer();\r
\r
- for (int i = 0; i < sequence.getSequence().length(); i++) {\r
- if (!jalview.util.Comparison.isGap(sequence.getCharAt(i))) {\r
+ for (int i = 0; i < sequence.getSequence().length(); i++)\r
+ {\r
+ if (!jalview.util.Comparison.isGap(sequence.getCharAt(i)))\r
+ {\r
nonGapped.append(sequence.getCharAt(i));\r
}\r
}\r
\r
int absStart = seqString.toString().indexOf(nonGapped.toString());\r
\r
- if (absStart == -1) {\r
+ if (absStart == -1)\r
+ {\r
unknownSequences.add(sequence.getName());\r
features = null;\r
sbuffer.append(sequence.getName() +\r
absStart += 1;\r
\r
if ((absStart != sequence.getStart()) ||\r
- (absEnd != sequence.getEnd())) {\r
+ (absEnd != sequence.getEnd()))\r
+ {\r
sbuffer.append("Updated: " + sequence.getName() + " " +\r
sequence.getStart() + "/" + sequence.getEnd() +\r
" to " + absStart + "/" + absEnd + "\n");\r
sequence.setEnd(absEnd);\r
}\r
\r
- if (result[r].indexOf("</entry>") > -1) {\r
- if (features != null) {\r
+ if (result[r].indexOf("</entry>") > -1)\r
+ {\r
+ if (features != null)\r
+ {\r
sequence.setSequenceFeatures(features);\r
}\r
\r
features = null;\r
sequence = null;\r
\r
- if (out != null) {\r
- try {\r
+ if (out != null)\r
+ {\r
+ try\r
+ {\r
out.writeBytes("</entry>\n");\r
- } catch (Exception ex) {\r
+ }\r
+ catch (Exception ex)\r
+ {\r
}\r
}\r
}\r
}\r
}\r
\r
- void findMissingIds(AlignmentI align) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param align DOCUMENT ME!\r
+ */\r
+ void findMissingIds(AlignmentI align)\r
+ {\r
String data;\r
ArrayList cachedIds = new ArrayList();\r
\r
- try {\r
+ try\r
+ {\r
BufferedReader in = new BufferedReader(new FileReader(\r
jalview.bin.Cache.getProperty("UNIPROT_CACHE")));\r
\r
- while ((data = in.readLine()) != null) {\r
- if (data.indexOf("name") > -1) {\r
+ while ((data = in.readLine()) != null)\r
+ {\r
+ if (data.indexOf("name") > -1)\r
+ {\r
String name = parseElement(data, "<name>", null);\r
cachedIds.add(name);\r
}\r
}\r
- } catch (Exception ex) {\r
+ }\r
+ catch (Exception ex)\r
+ {\r
ex.printStackTrace();\r
}\r
\r
for (int i = 0; i < align.getHeight(); i++)\r
- if (!cachedIds.contains(align.getSequenceAt(i).getName())) {\r
+ if (!cachedIds.contains(align.getSequenceAt(i).getName()))\r
+ {\r
unknownSequences.add(align.getSequenceAt(i).getName());\r
}\r
}\r
\r
- void tryLocalCacheFirst(ArrayList ids, AlignmentI align) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param ids DOCUMENT ME!\r
+ * @param align DOCUMENT ME!\r
+ */\r
+ void tryLocalCacheFirst(ArrayList ids, AlignmentI align)\r
+ {\r
ArrayList cacheData = new ArrayList();\r
\r
- try {\r
+ try\r
+ {\r
BufferedReader in = new BufferedReader(new FileReader(\r
jalview.bin.Cache.getProperty("UNIPROT_CACHE")));\r
\r
// make sure we remove the ids from the list to retrieve from EBI\r
String data;\r
\r
- while ((data = in.readLine()) != null) {\r
- if (data.indexOf("name") > -1) {\r
+ while ((data = in.readLine()) != null)\r
+ {\r
+ if (data.indexOf("name") > -1)\r
+ {\r
String name = parseElement(data, "<name>", null);\r
\r
- if (ids.contains(name)) {\r
+ if (ids.contains(name))\r
+ {\r
cacheData.add("<entry>");\r
cacheData.add(data);\r
\r
- while (data.indexOf("</entry>") == -1) {\r
+ while (data.indexOf("</entry>") == -1)\r
+ {\r
data = in.readLine();\r
cacheData.add(data);\r
}\r
}\r
}\r
}\r
- } catch (Exception ex) {\r
+ }\r
+ catch (Exception ex)\r
+ {\r
ex.printStackTrace();\r
}\r
\r
String[] localData = new String[cacheData.size()];\r
cacheData.toArray(localData);\r
\r
- if ((localData != null) && (localData.length > 0)) {\r
+ if ((localData != null) && (localData.length > 0))\r
+ {\r
ReadUniprotFile(localData, null, align);\r
}\r
}\r
\r
- String parseValue(String line, String tag, RandomAccessFile out) {\r
- if (out != null) {\r
- try {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param line DOCUMENT ME!\r
+ * @param tag DOCUMENT ME!\r
+ * @param out DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ String parseValue(String line, String tag, RandomAccessFile out)\r
+ {\r
+ if (out != null)\r
+ {\r
+ try\r
+ {\r
out.writeBytes(line + "\n");\r
- } catch (Exception ex) {\r
+ }\r
+ catch (Exception ex)\r
+ {\r
}\r
}\r
\r
int index = line.indexOf(tag) + tag.length() + 1;\r
\r
- if (index == tag.length()) {\r
+ if (index == tag.length())\r
+ {\r
return "";\r
}\r
\r
return line.substring(index, line.indexOf("\"", index + 1));\r
}\r
\r
- String parseElement(String line, String tag, RandomAccessFile out) {\r
- if (out != null) {\r
- try {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param line DOCUMENT ME!\r
+ * @param tag DOCUMENT ME!\r
+ * @param out DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ String parseElement(String line, String tag, RandomAccessFile out)\r
+ {\r
+ if (out != null)\r
+ {\r
+ try\r
+ {\r
out.writeBytes(line + "\n");\r
- } catch (Exception ex) {\r
+ }\r
+ catch (Exception ex)\r
+ {\r
}\r
}\r
\r
git://source.jalview.org / jalview.git / blobdiff