* 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
+\r
+import jalview.gui.*;\r
+\r
+import jalview.io.*;\r
+\r
import java.io.*;\r
+\r
import java.util.*;\r
+\r
import javax.swing.*;\r
-import jalview.io.*;\r
-import jalview.gui.*;\r
-import jalview.datamodel.*;\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
- unknownSequences = new ArrayList();\r
- this.align = align;\r
- this.ap = ap;\r
- Thread thread = new Thread(this);\r
- thread.start();\r
- }\r
-\r
- public void run()\r
-{\r
-\r
- String cache = jalview.bin.Cache.getProperty("UNIPROT_CACHE");\r
-\r
- RandomAccessFile out = null;\r
-\r
- try{\r
- if (cache == null)\r
- {\r
- jalview.bin.Cache.setProperty("UNIPROT_CACHE", System.getProperty("user.home")+"/uniprot.xml");\r
- cache = jalview.bin.Cache.getProperty("UNIPROT_CACHE");\r
- }\r
\r
+public class SequenceFeatureFetcher implements Runnable {\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
+ unknownSequences = new ArrayList();\r
+ this.align = align;\r
+ this.ap = ap;\r
\r
- File test = new File(cache);\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
- }\r
- else\r
- {\r
- out = new RandomAccessFile(cache, "rw");\r
- // open exisiting cache and remove </UNIPROT_CACHE> from the end\r
- long lastLine = 0;\r
- String data;\r
- while ( (data = out.readLine()) != null)\r
- {\r
- if (data.indexOf("</entry>") > -1)\r
- lastLine = out.getFilePointer();\r
-\r
- }\r
- out.seek(lastLine);\r
+ Thread thread = new Thread(this);\r
+ thread.start();\r
}\r
\r
- int seqIndex = 0;\r
- Vector sequences = align.getSequences();\r
+ public void run() {\r
+ String cache = jalview.bin.Cache.getProperty("UNIPROT_CACHE");\r
\r
- while (seqIndex < sequences.size())\r
- {\r
- ArrayList ids = new ArrayList();\r
- for (int i = 0; seqIndex < sequences.size() && i < 50; seqIndex++, i++)\r
- {\r
- SequenceI sequence = (SequenceI) sequences.get(seqIndex);\r
- ids.add(sequence.getName());\r
- }\r
+ RandomAccessFile out = null;\r
\r
- tryLocalCacheFirst(ids, align);\r
+ try {\r
+ if (cache == null) {\r
+ jalview.bin.Cache.setProperty("UNIPROT_CACHE",\r
+ System.getProperty("user.home") + "/uniprot.xml");\r
+ cache = jalview.bin.Cache.getProperty("UNIPROT_CACHE");\r
+ }\r
\r
- if (ids.size() > 0)\r
- {\r
- StringBuffer remainingIds = new StringBuffer("uniprot:");\r
- for (int i = 0; i < ids.size(); i++)\r
- remainingIds.append(ids.get(i) + ";");\r
+ File test = new File(cache);\r
\r
- EBIFetchClient ebi = new EBIFetchClient();\r
- String[] result = ebi.fetchData(remainingIds.toString(), "xml", null);\r
+ if (!test.exists()) {\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
+ out = new RandomAccessFile(cache, "rw");\r
\r
- if(result!=null)\r
- ReadUniprotFile(result, out, align);\r
- }\r
+ // open exisiting cache and remove </UNIPROT_CACHE> from the end\r
+ long lastLine = 0;\r
+ String data;\r
\r
- }\r
+ while ((data = out.readLine()) != null) {\r
+ if (data.indexOf("</entry>") > -1) {\r
+ lastLine = out.getFilePointer();\r
+ }\r
+ }\r
\r
- if (out != null)\r
- {\r
- out.writeBytes("</UNIPROT_CACHE>\n");\r
- out.close();\r
- }\r
- }catch(Exception ex){ex.printStackTrace();}\r
+ out.seek(lastLine);\r
+ }\r
\r
- ap.repaint();\r
- findMissingIds(align);\r
- if(sbuffer.length()>0)\r
- {\r
- output.setText("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
- +"Save your alignment to maintain the updated id.\n\n"+sbuffer.toString());\r
- Desktop.addInternalFrame(output, "Sequence names updated ", 600,300);\r
+ int seqIndex = 0;\r
+ Vector sequences = align.getSequences();\r
\r
- }\r
+ while (seqIndex < sequences.size()) {\r
+ ArrayList ids = new ArrayList();\r
\r
- if(unknownSequences.size()>0)\r
- {\r
- //ignore for now!!!!!!!!!!\r
- // WSWUBlastClient blastClient = new WSWUBlastClient(align, unknownSequences);\r
- }\r
+ for (int i = 0; (seqIndex < sequences.size()) && (i < 50);\r
+ seqIndex++, i++) {\r
+ SequenceI sequence = (SequenceI) sequences.get(seqIndex);\r
+ ids.add(sequence.getName());\r
+ }\r
\r
-}\r
+ tryLocalCacheFirst(ids, align);\r
+\r
+ if (ids.size() > 0) {\r
+ StringBuffer remainingIds = new StringBuffer("uniprot:");\r
\r
-void ReadUniprotFile(String [] result, RandomAccessFile out, AlignmentI align)\r
-{\r
- SequenceI sequence = null;\r
- Vector features = null;\r
- String type, description, status, start, end, pdb = null;\r
-\r
-\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
- filePointer=out.getFilePointer();\r
- out.writeBytes("<entry>\n");\r
- }catch(Exception ex){}\r
-\r
- String seqName = parseElement( result[r], "<name>" , out);\r
- sequence = align.findName( seqName ) ;\r
- if(sequence==null)\r
- {\r
- sequence = align.findName( seqName.substring(0, seqName.indexOf('_')));\r
- if(sequence!=null)\r
- {\r
- sbuffer.append("changing "+sequence.getName()+" to "+seqName+"\n");\r
- sequence.setName(seqName);\r
+ for (int i = 0; i < ids.size(); i++)\r
+ remainingIds.append(ids.get(i) + ";");\r
+\r
+ EBIFetchClient ebi = new EBIFetchClient();\r
+ String[] result = ebi.fetchData(remainingIds.toString(),\r
+ "xml", null);\r
+\r
+ if (result != null) {\r
+ ReadUniprotFile(result, out, align);\r
+ }\r
+ }\r
+ }\r
+\r
+ if (out != null) {\r
+ out.writeBytes("</UNIPROT_CACHE>\n");\r
+ out.close();\r
+ }\r
+ } catch (Exception ex) {\r
+ ex.printStackTrace();\r
}\r
- }\r
- if(sequence==null)\r
- {\r
- sbuffer.append("UNIPROT updated suggestion is "+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 { out.setLength(filePointer); } catch (Exception ex) {}\r
- // now skip to next entry\r
- while( result[r].indexOf("</entry>")==-1)\r
- r++;\r
- }\r
-\r
- features = new Vector();\r
- type=""; start="0"; end="0"; description=""; status=""; pdb="";\r
\r
+ ap.repaint();\r
+ findMissingIds(align);\r
+\r
+ if (sbuffer.length() > 0) {\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
+ "Save your alignment to maintain the updated id.\n\n" +\r
+ sbuffer.toString());\r
+ Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);\r
+ }\r
+\r
+ if (unknownSequences.size() > 0) {\r
+ //ignore for now!!!!!!!!!!\r
+ // WSWUBlastClient blastClient = new WSWUBlastClient(align, unknownSequences);\r
+ }\r
}\r
\r
- if(sequence==null)\r
- continue;\r
-\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
- {\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
- {\r
- r++; //<location>\r
- }\r
- // r++;\r
- if(result[r].indexOf("begin")>-1)\r
- {\r
- start = parseValue( result[r], "position=" , out);\r
- end = parseValue( result[++r], "position=" , out);\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
- if(out!=null)\r
- try{ out.writeBytes("</feature>\n"); }catch(Exception ex){}\r
-\r
- SequenceFeature sf = new SequenceFeature(type,\r
- sstart,\r
- eend,\r
- description,\r
- status);\r
- features.add(sf);\r
- }\r
-\r
- if(result[r].indexOf("<sequence")>-1)\r
- {\r
- StringBuffer seqString = new StringBuffer();\r
-\r
- if(out!=null)\r
- try { out.writeBytes(result[r]+"\n"); } catch (Exception ex){}\r
-\r
- while(result[++r].indexOf("</sequence>")==-1)\r
- {\r
- seqString.append(result[r]);\r
- if(out!=null)\r
- try { out.writeBytes(result[r]+"\n"); } catch (Exception ex){}\r
- }\r
-\r
- if(out!=null)\r
- try { out.writeBytes(result[r]+"\n"); } catch (Exception ex){}\r
-\r
- StringBuffer nonGapped = new StringBuffer();\r
- for (int i = 0; i < sequence.getSequence().length(); i++)\r
- {\r
- if (!jalview.util.Comparison.isGap(sequence.getCharAt(i)))\r
- nonGapped.append(sequence.getCharAt(i));\r
- }\r
-\r
- int absStart = seqString.toString().indexOf(nonGapped.toString());\r
- if(absStart==-1)\r
- {\r
- unknownSequences.add(sequence.getName());\r
- features = null;\r
- sbuffer.append(sequence.getName()+ " SEQUENCE NOT %100 MATCH \n");\r
- continue;\r
- }\r
-\r
- int absEnd = absStart + nonGapped.toString().length();\r
- absStart+=1;\r
-\r
- if(absStart!=sequence.getStart() || absEnd!=sequence.getEnd())\r
- sbuffer.append("Updated: "+sequence.getName()+" "+\r
- sequence.getStart()+"/"+sequence.getEnd()+" to "+ absStart+"/"+absEnd+"\n");\r
-\r
-\r
- sequence.setStart(absStart);\r
- sequence.setEnd(absEnd);\r
-\r
- }\r
-\r
- if(result[r].indexOf("</entry>")>-1)\r
- {\r
- if(features!=null)\r
- sequence.setSequenceFeatures( features );\r
- features = null;\r
- sequence = null;\r
- if(out!=null)\r
- try{ out.writeBytes("</entry>\n"); }catch(Exception ex){}\r
-\r
- }\r
- }\r
-}\r
+ void ReadUniprotFile(String[] result, RandomAccessFile out, AlignmentI align) {\r
+ SequenceI sequence = null;\r
+ Vector features = null;\r
+ String type;\r
+ String description;\r
+ String status;\r
+ String start;\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
+ long filePointer = 0;\r
+\r
+ if (out != null) {\r
+ try {\r
+ filePointer = out.getFilePointer();\r
+ out.writeBytes("<entry>\n");\r
+ } catch (Exception ex) {\r
+ }\r
+ }\r
+\r
+ String seqName = parseElement(result[r], "<name>", out);\r
+ sequence = align.findName(seqName);\r
+\r
+ if (sequence == null) {\r
+ sequence = align.findName(seqName.substring(0,\r
+ seqName.indexOf('_')));\r
+\r
+ if (sequence != null) {\r
+ sbuffer.append("changing " + sequence.getName() +\r
+ " to " + seqName + "\n");\r
+ sequence.setName(seqName);\r
+ }\r
+ }\r
+\r
+ if (sequence == null) {\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
+ out.setLength(filePointer);\r
+ } catch (Exception ex) {\r
+ }\r
+\r
+ // now skip to next entry\r
+ while (result[r].indexOf("</entry>") == -1)\r
+ r++;\r
+ }\r
+\r
+ features = new Vector();\r
+ type = "";\r
+ start = "0";\r
+ end = "0";\r
+ description = "";\r
+ status = "";\r
+ pdb = "";\r
+ }\r
+\r
+ if (sequence == null) {\r
+ continue;\r
+ }\r
+\r
+ if (result[r].indexOf("<property type=\"pdb accession\"") > -1) {\r
+ pdb = parseValue(result[r], "value=", out);\r
+ sequence.setPDBId(pdb);\r
+ }\r
+\r
+ if (result[r].indexOf("feature type") > -1) {\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
+ r++; //<location>\r
+ }\r
+\r
+ // r++;\r
+ if (result[r].indexOf("begin") > -1) {\r
+ start = parseValue(result[r], "position=", out);\r
+ end = parseValue(result[++r], "position=", out);\r
+ } else {\r
+ start = parseValue(result[r], "position=", out);\r
+ end = parseValue(result[r], "position=", null);\r
+ }\r
+\r
+ int sstart = Integer.parseInt(start);\r
+ int eend = Integer.parseInt(end);\r
+\r
+ if (out != null) {\r
+ try {\r
+ out.writeBytes("</feature>\n");\r
+ } catch (Exception ex) {\r
+ }\r
+ }\r
+\r
+ SequenceFeature sf = new SequenceFeature(type, sstart, eend,\r
+ description, status);\r
+ features.add(sf);\r
+ }\r
+\r
+ if (result[r].indexOf("<sequence") > -1) {\r
+ StringBuffer seqString = new StringBuffer();\r
+\r
+ if (out != null) {\r
+ try {\r
+ out.writeBytes(result[r] + "\n");\r
+ } catch (Exception ex) {\r
+ }\r
+ }\r
+\r
+ while (result[++r].indexOf("</sequence>") == -1) {\r
+ seqString.append(result[r]);\r
+\r
+ if (out != null) {\r
+ try {\r
+ out.writeBytes(result[r] + "\n");\r
+ } catch (Exception ex) {\r
+ }\r
+ }\r
+ }\r
+\r
+ if (out != null) {\r
+ try {\r
+ out.writeBytes(result[r] + "\n");\r
+ } catch (Exception ex) {\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
+ nonGapped.append(sequence.getCharAt(i));\r
+ }\r
+ }\r
+\r
+ int absStart = seqString.toString().indexOf(nonGapped.toString());\r
+\r
+ if (absStart == -1) {\r
+ unknownSequences.add(sequence.getName());\r
+ features = null;\r
+ sbuffer.append(sequence.getName() +\r
+ " SEQUENCE NOT %100 MATCH \n");\r
+\r
+ continue;\r
+ }\r
+\r
+ int absEnd = absStart + nonGapped.toString().length();\r
+ absStart += 1;\r
+\r
+ if ((absStart != sequence.getStart()) ||\r
+ (absEnd != sequence.getEnd())) {\r
+ sbuffer.append("Updated: " + sequence.getName() + " " +\r
+ sequence.getStart() + "/" + sequence.getEnd() +\r
+ " to " + absStart + "/" + absEnd + "\n");\r
+ }\r
+\r
+ sequence.setStart(absStart);\r
+ sequence.setEnd(absEnd);\r
+ }\r
+\r
+ if (result[r].indexOf("</entry>") > -1) {\r
+ if (features != null) {\r
+ sequence.setSequenceFeatures(features);\r
+ }\r
+\r
+ features = null;\r
+ sequence = null;\r
+\r
+ if (out != null) {\r
+ try {\r
+ out.writeBytes("</entry>\n");\r
+ } catch (Exception ex) {\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
\r
-void findMissingIds(AlignmentI align)\r
-{\r
- String data;\r
- ArrayList cachedIds = new ArrayList();\r
-\r
- try\r
- {\r
- BufferedReader in = new BufferedReader(\r
- new FileReader(jalview.bin.Cache.getProperty("UNIPROT_CACHE")));\r
-\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
+ void findMissingIds(AlignmentI align) {\r
+ String data;\r
+ ArrayList cachedIds = new ArrayList();\r
+\r
+ try {\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
+ String name = parseElement(data, "<name>", null);\r
+ cachedIds.add(name);\r
+ }\r
+ }\r
+ } catch (Exception ex) {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ for (int i = 0; i < align.getHeight(); i++)\r
+ if (!cachedIds.contains(align.getSequenceAt(i).getName())) {\r
+ unknownSequences.add(align.getSequenceAt(i).getName());\r
+ }\r
}\r
- }\r
- catch (Exception ex)\r
- { ex.printStackTrace(); }\r
\r
- for(int i=0; i<align.getHeight(); i++)\r
- if( !cachedIds.contains( align.getSequenceAt(i).getName() ) )\r
- unknownSequences.add( align.getSequenceAt(i).getName() );\r
+ void tryLocalCacheFirst(ArrayList ids, AlignmentI align) {\r
+ ArrayList cacheData = new ArrayList();\r
\r
+ try {\r
+ BufferedReader in = new BufferedReader(new FileReader(\r
+ jalview.bin.Cache.getProperty("UNIPROT_CACHE")));\r
\r
-}\r
+ // read through cache file, if the cache has sequences we're looking for\r
+ // add the lines to a new String array, Readthis new array and\r
+ // make sure we remove the ids from the list to retrieve from EBI\r
+ String data;\r
\r
-void tryLocalCacheFirst(ArrayList ids, AlignmentI align)\r
-{\r
- ArrayList cacheData = new ArrayList();\r
- try{\r
- BufferedReader in = new BufferedReader(\r
- new FileReader(jalview.bin.Cache.getProperty("UNIPROT_CACHE")));\r
-\r
- // read through cache file, if the cache has sequences we're looking for\r
- // add the lines to a new String array, Readthis new array and\r
- // make sure we remove the ids from the list to retrieve from EBI\r
- String data;\r
- while( ( data=in.readLine())!=null)\r
- {\r
- if(data.indexOf("name")>-1)\r
- {\r
- String name = parseElement( data, "<name>" , null) ;\r
- if(ids.contains( name ) )\r
- {\r
- cacheData.add("<entry>");\r
- cacheData.add(data);\r
- while( data.indexOf("</entry>")==-1)\r
- {\r
- data = in.readLine();\r
- cacheData.add(data);\r
- }\r
- cacheData.add(data);\r
-\r
- ids.remove( name );\r
- }\r
- }\r
- }\r
- }\r
- catch(Exception ex){ex.printStackTrace();}\r
+ while ((data = in.readLine()) != null) {\r
+ if (data.indexOf("name") > -1) {\r
+ String name = parseElement(data, "<name>", null);\r
\r
- String [] localData = new String[cacheData.size()];\r
- cacheData.toArray( localData );\r
- if(localData!=null && localData.length>0)\r
- ReadUniprotFile(localData, null, align);\r
-}\r
+ if (ids.contains(name)) {\r
+ cacheData.add("<entry>");\r
+ cacheData.add(data);\r
\r
+ while (data.indexOf("</entry>") == -1) {\r
+ data = in.readLine();\r
+ cacheData.add(data);\r
+ }\r
\r
-String parseValue(String line, String tag, RandomAccessFile out)\r
-{\r
- if(out!=null)\r
- try{ out.writeBytes(line+"\n"); }catch(Exception ex){}\r
+ cacheData.add(data);\r
\r
+ ids.remove(name);\r
+ }\r
+ }\r
+ }\r
+ } catch (Exception ex) {\r
+ ex.printStackTrace();\r
+ }\r
\r
- int index = line.indexOf(tag)+tag.length()+1;\r
- if(index==tag.length())\r
- return "";\r
+ String[] localData = new String[cacheData.size()];\r
+ cacheData.toArray(localData);\r
\r
- return line.substring( index, line.indexOf("\"", index+1) );\r
-}\r
+ if ((localData != null) && (localData.length > 0)) {\r
+ ReadUniprotFile(localData, null, align);\r
+ }\r
+ }\r
+\r
+ String parseValue(String line, String tag, RandomAccessFile out) {\r
+ if (out != null) {\r
+ try {\r
+ out.writeBytes(line + "\n");\r
+ } catch (Exception ex) {\r
+ }\r
+ }\r
\r
+ int index = line.indexOf(tag) + tag.length() + 1;\r
\r
-String parseElement(String line, String tag, RandomAccessFile out)\r
-{\r
- if (out != null)\r
- try\r
- {\r
- out.writeBytes(line + "\n");\r
+ if (index == tag.length()) {\r
+ return "";\r
+ }\r
+\r
+ return line.substring(index, line.indexOf("\"", index + 1));\r
}\r
- catch (Exception ex)\r
- {}\r
\r
- int index = line.indexOf(tag) + tag.length();\r
- return line.substring(index, line.indexOf("</"));\r
+ String parseElement(String line, String tag, RandomAccessFile out) {\r
+ if (out != null) {\r
+ try {\r
+ out.writeBytes(line + "\n");\r
+ } catch (Exception ex) {\r
+ }\r
+ }\r
\r
- }\r
+ int index = line.indexOf(tag) + tag.length();\r
+\r
+ return line.substring(index, line.indexOf("</"));\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff