moved to jalview.io

diff --git a/src/jalview/analysis/SequenceFeatureFetcher.java b/src/jalview/analysis/SequenceFeatureFetcher.java
deleted file mode 100755 (executable)
index 2c0aaac..0000000
--- a/src/jalview/analysis/SequenceFeatureFetcher.java
+++ /dev/null
@@ -1,372 +0,0 @@
-package jalview.analysis;\r
-\r
-import java.io.*;\r
-import java.util.*;\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
-  JInternalFrame outputFrame = new JInternalFrame();\r
-  CutAndPasteTransfer output = new CutAndPasteTransfer(false);\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
-\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
-    }\r
-\r
-    int seqIndex = 0;\r
-    Vector sequences = align.getSequences();\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
-\r
-      tryLocalCacheFirst(ids, align);\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
-\r
-         EBIFetchClient ebi = new EBIFetchClient();\r
-         String[] result = ebi.fetchData(remainingIds.toString(), "xml", null);\r
-\r
-        if(result!=null)\r
-          ReadUniprotFile(result, out, align);\r
-      }\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
-\r
-  ap.repaint();\r
-  findMissingIds(align);\r
-  if(sbuffer.length()>0)\r
-  {\r
-    output.formatForOutput();\r
-    outputFrame.setContentPane(output);\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(outputFrame, "Sequence names updated ", 600,300);\r
-\r
-  }\r
-\r
-  if(unknownSequences.size()>0)\r
-  {\r
-    //ignore for now!!!!!!!!!!\r
-  //  WSWUBlastClient blastClient = new WSWUBlastClient(align, unknownSequences);\r
-  }\r
-\r
-}\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
-        }\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
-    }\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
-\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
-    }\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
-\r
-\r
-}\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
-\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
-\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
-\r
-\r
-  int index = line.indexOf(tag)+tag.length()+1;\r
-  if(index==tag.length())\r
-    return "";\r
-\r
-  return line.substring( index, line.indexOf("\"", index+1) );\r
-}\r
-\r
-\r
-String parseElement(String line, String tag, RandomAccessFile out)\r
-{\r
-  if (out != null)\r
-    try\r
-    {\r
-      out.writeBytes(line + "\n");\r
-    }\r
-    catch (Exception ex)\r
-    {}\r
-\r
-  int index = line.indexOf(tag) + tag.length();\r
-  return line.substring(index, line.indexOf("</"));\r
-}\r
-\r
-\r
-}\r