X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FSequenceFeatureFetcher.java;h=bb404d8310657e0e2e311a1cb50f764ace795c8d;hb=dcd8d3212242ef3bde7ff9d865f9dfb859407a30;hp=afe7b6e191db8614f5e1ac913966439a8453bc1e;hpb=b618755c67d798ace34ebd6d0f384e913e8574c9;p=jalview.git

diff --git a/src/jalview/io/SequenceFeatureFetcher.java b/src/jalview/io/SequenceFeatureFetcher.java
index afe7b6e..bb404d8 100755
--- a/src/jalview/io/SequenceFeatureFetcher.java
+++ b/src/jalview/io/SequenceFeatureFetcher.java
@@ -1,370 +1,417 @@
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+*/
 package jalview.io;
 
+import jalview.datamodel.*;
+
+import jalview.gui.*;
+
+import jalview.io.*;
+
 import java.io.*;
+
 import java.util.*;
-import javax.swing.*;
-import jalview.io.*;
-import jalview.gui.*;
-import jalview.datamodel.*;
 
-public class SequenceFeatureFetcher implements Runnable
-{
-  AlignmentI align;
-  AlignmentPanel ap;
-  ArrayList unknownSequences;
-  JInternalFrame outputFrame = new JInternalFrame();
-  CutAndPasteTransfer output = new CutAndPasteTransfer();
-  StringBuffer sbuffer = new StringBuffer();
-
-  public SequenceFeatureFetcher(AlignmentI align, AlignmentPanel ap)
-  {
-    unknownSequences = new ArrayList();
-    this.align = align;
-    this.ap = ap;
-    Thread thread = new Thread(this);
-    thread.start();
-  }
-
-  public void run()
-{
-
-  String cache = jalview.bin.Cache.getProperty("UNIPROT_CACHE");
-
-  RandomAccessFile out = null;
-
-  try{
-    if (cache == null)
-    {
-      jalview.bin.Cache.setProperty("UNIPROT_CACHE", System.getProperty("user.home")+"/uniprot.xml");
-      cache = jalview.bin.Cache.getProperty("UNIPROT_CACHE");
-    }
 
+public class SequenceFeatureFetcher implements Runnable {
+    AlignmentI align;
+    AlignmentPanel ap;
+    ArrayList unknownSequences;
+    CutAndPasteTransfer output = new CutAndPasteTransfer();
+    StringBuffer sbuffer = new StringBuffer();
 
+    public SequenceFeatureFetcher(AlignmentI align, AlignmentPanel ap) {
+        unknownSequences = new ArrayList();
+        this.align = align;
+        this.ap = ap;
 
-    File test = new File(cache);
-    if( !test.exists() )
-    {
-      out = new RandomAccessFile(cache, "rw");
-      out.writeBytes("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
-      out.writeBytes("<UNIPROT_CACHE>\n");
-    }
-    else
-    {
-      out = new RandomAccessFile(cache, "rw");
-      // open exisiting cache and remove </UNIPROT_CACHE> from the end
-      long lastLine = 0;
-      String data;
-      while ( (data = out.readLine()) != null)
-      {
-        if (data.indexOf("</entry>") > -1)
-          lastLine = out.getFilePointer();
-
-      }
-      out.seek(lastLine);
+        Thread thread = new Thread(this);
+        thread.start();
     }
 
-    int seqIndex = 0;
-    Vector sequences = align.getSequences();
+    public void run() {
+        String cache = jalview.bin.Cache.getProperty("UNIPROT_CACHE");
 
-    while (seqIndex < sequences.size())
-    {
-      ArrayList ids = new ArrayList();
-      for (int i = 0; seqIndex < sequences.size() && i < 50; seqIndex++, i++)
-      {
-        SequenceI sequence = (SequenceI) sequences.get(seqIndex);
-        ids.add(sequence.getName());
-      }
+        RandomAccessFile out = null;
 
-      tryLocalCacheFirst(ids, align);
+        try {
+            if (cache == null) {
+                jalview.bin.Cache.setProperty("UNIPROT_CACHE",
+                    System.getProperty("user.home") + "/.jalview.uniprot.xml");
+                cache = jalview.bin.Cache.getProperty("UNIPROT_CACHE");
+            }
 
-      if (ids.size() > 0)
-      {
-        StringBuffer remainingIds = new StringBuffer("uniprot:");
-        for (int i = 0; i < ids.size(); i++)
-          remainingIds.append(ids.get(i) + ";");
+            File test = new File(cache);
 
-         EBIFetchClient ebi = new EBIFetchClient();
-         String[] result = ebi.fetchData(remainingIds.toString(), "xml", null);
+            if (!test.exists()) {
+                out = new RandomAccessFile(cache, "rw");
+                out.writeBytes("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
+                out.writeBytes("<UNIPROT_CACHE>\n");
+            } else {
+                out = new RandomAccessFile(cache, "rw");
 
-        if(result!=null)
-          ReadUniprotFile(result, out, align);
-      }
+                // open exisiting cache and remove </UNIPROT_CACHE> from the end
+                long lastLine = 0;
+                String data;
 
-    }
+                while ((data = out.readLine()) != null) {
+                    if (data.indexOf("</entry>") > -1) {
+                        lastLine = out.getFilePointer();
+                    }
+                }
 
-    if (out != null)
-    {
-      out.writeBytes("</UNIPROT_CACHE>\n");
-      out.close();
-    }
-  }catch(Exception ex){ex.printStackTrace();}
-
-  ap.repaint();
-  findMissingIds(align);
-  if(sbuffer.length()>0)
-  {
-    outputFrame.setContentPane(output);
-    output.setText("Your sequences have been matched to Uniprot. Some of the ids have been\n"
-                   +"altered, most likely the start/end residue will have been updated.\n"
-                   +"Save your alignment to maintain the updated id.\n\n"+sbuffer.toString());
-  Desktop.addInternalFrame(outputFrame, "Sequence names updated ", 600,300);
-
-  }
-
-  if(unknownSequences.size()>0)
-  {
-    //ignore for now!!!!!!!!!!
-  //  WSWUBlastClient blastClient = new WSWUBlastClient(align, unknownSequences);
-  }
+                out.seek(lastLine);
+            }
 
-}
+            int seqIndex = 0;
+            Vector sequences = align.getSequences();
+
+            while (seqIndex < sequences.size()) {
+                ArrayList ids = new ArrayList();
+
+                for (int i = 0; (seqIndex < sequences.size()) && (i < 50);
+                        seqIndex++, i++) {
+                    SequenceI sequence = (SequenceI) sequences.get(seqIndex);
+                    ids.add(sequence.getName());
+                }
+
+                tryLocalCacheFirst(ids, align);
+
+                if (ids.size() > 0) {
+                    StringBuffer remainingIds = new StringBuffer("uniprot:");
+
+                    for (int i = 0; i < ids.size(); i++)
+                        remainingIds.append(ids.get(i) + ";");
+
+                    EBIFetchClient ebi = new EBIFetchClient();
+                    String[] result = ebi.fetchData(remainingIds.toString(),
+                            "xml", null);
+
+                    if (result != null) {
+                        ReadUniprotFile(result, out, align);
+                    }
+                }
+            }
+
+            if (out != null) {
+                out.writeBytes("</UNIPROT_CACHE>\n");
+                out.close();
+            }
+        } catch (Exception ex) {
+            ex.printStackTrace();
+        }
+
+        jalview.gui.PaintRefresher.Refresh(null, align);
+        findMissingIds(align);
 
-void ReadUniprotFile(String [] result, RandomAccessFile out, AlignmentI align)
-{
-  SequenceI sequence = null;
-  Vector features = null;
-  String type, description, status, start, end, pdb = null;
-
-
-  for (int r = 0; r < result.length; r++)
-  {
-    if(sequence==null && result[r].indexOf("<name>")>-1)
-    {
-      long filePointer = 0;
-
-      if(out!=null)
-      try{
-        filePointer=out.getFilePointer();
-        out.writeBytes("<entry>\n");
-      }catch(Exception ex){}
-
-      String seqName = parseElement( result[r], "<name>" , out);
-      sequence = align.findName( seqName ) ;
-      if(sequence==null)
-      {
-        sequence = align.findName( seqName.substring(0, seqName.indexOf('_')));
-        if(sequence!=null)
-        {
-          sbuffer.append("changing "+sequence.getName()+" to "+seqName+"\n");
-          sequence.setName(seqName);
+        if (sbuffer.length() > 0) {
+            output.setText(
+                "Your sequences have been matched to Uniprot. Some of the ids have been\n" +
+                "altered, most likely the start/end residue will have been updated.\n" +
+                "Save your alignment to maintain the updated id.\n\n" +
+                sbuffer.toString());
+            Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);
         }
-      }
-      if(sequence==null)
-      {
-        sbuffer.append("UNIPROT updated suggestion is "+result[r]+"\n");
-        sequence = align.findName( result[r] ) ;
-
-        // this entry has been suggested by ebi.
-        // doesn't match id in alignment file
-        try   { out.setLength(filePointer);  }  catch (Exception ex) {}
-        // now skip to next entry
-        while( result[r].indexOf("</entry>")==-1)
-          r++;
-      }
-
-      features = new Vector();
-      type=""; start="0"; end="0"; description=""; status=""; pdb="";
 
+        if (unknownSequences.size() > 0) {
+            //ignore for now!!!!!!!!!!
+            //  WSWUBlastClient blastClient = new WSWUBlastClient(align, unknownSequences);
+        }
     }
 
-    if(sequence==null)
-      continue;
-
-     if( result[r].indexOf("<property type=\"pdb accession\"")>-1)
-     {
-       pdb = parseValue( result[r], "value=" , out);
-       sequence.setPDBId(pdb);
-     }
-
-     if(result[r].indexOf("feature type")>-1)
-     {
-       type = parseValue( result[r], "type=" , out);
-       description = parseValue( result[r], "description=" , null );
-       status = parseValue ( result[r], "status=", null);
-
-       while( result[r].indexOf("position")==-1)
-       {
-           r++;  //<location>
-       }
-      // r++;
-       if(result[r].indexOf("begin")>-1)
-       {
-         start = parseValue( result[r], "position=" , out);
-         end = parseValue( result[++r], "position=" , out);
-       }
-       else
-       {
-         start = parseValue( result[r], "position=" , out);
-         end = parseValue(   result[r], "position=" , null);
-       }
-       int sstart = Integer.parseInt(start);
-       int eend = Integer.parseInt(end);
-       if(out!=null)
-         try{ out.writeBytes("</feature>\n"); }catch(Exception ex){}
-
-         SequenceFeature sf = new SequenceFeature(type,
-             sstart,
-             eend,
-             description,
-             status);
-         features.add(sf);
-     }
-
-     if(result[r].indexOf("<sequence")>-1)
-     {
-       StringBuffer seqString = new StringBuffer();
-
-       if(out!=null)
-         try  {  out.writeBytes(result[r]+"\n"); }   catch (Exception ex){}
-
-       while(result[++r].indexOf("</sequence>")==-1)
-       {
-         seqString.append(result[r]);
-         if(out!=null)
-         try  {  out.writeBytes(result[r]+"\n"); }   catch (Exception ex){}
-       }
-
-       if(out!=null)
-         try  {  out.writeBytes(result[r]+"\n"); }   catch (Exception ex){}
-
-       StringBuffer nonGapped = new StringBuffer();
-       for (int i = 0; i < sequence.getSequence().length(); i++)
-       {
-         if (!jalview.util.Comparison.isGap(sequence.getCharAt(i)))
-           nonGapped.append(sequence.getCharAt(i));
-       }
-
-       int absStart = seqString.toString().indexOf(nonGapped.toString());
-       if(absStart==-1)
-       {
-         unknownSequences.add(sequence.getName());
-         features = null;
-         sbuffer.append(sequence.getName()+ " SEQUENCE NOT %100 MATCH \n");
-         continue;
-       }
-
-       int absEnd =   absStart + nonGapped.toString().length();
-       absStart+=1;
-
-       if(absStart!=sequence.getStart() || absEnd!=sequence.getEnd())
-         sbuffer.append("Updated: "+sequence.getName()+" "+
-                           sequence.getStart()+"/"+sequence.getEnd()+"  to  "+ absStart+"/"+absEnd+"\n");
-
-
-       sequence.setStart(absStart);
-       sequence.setEnd(absEnd);
-
-     }
-
-     if(result[r].indexOf("</entry>")>-1)
-     {
-       if(features!=null)
-         sequence.setSequenceFeatures( features );
-       features = null;
-       sequence = null;
-       if(out!=null)
-         try{  out.writeBytes("</entry>\n"); }catch(Exception ex){}
-
-     }
-  }
-}
+    void ReadUniprotFile(String[] result, RandomAccessFile out, AlignmentI align) {
+        SequenceI sequence = null;
+        Vector features = null;
+        String type;
+        String description;
+        String status;
+        String start;
+        String end;
+        String pdb = null;
+
+        for (int r = 0; r < result.length; r++) {
+            if ((sequence == null) && (result[r].indexOf("<name>") > -1)) {
+                long filePointer = 0;
+
+                if (out != null) {
+                    try {
+                        filePointer = out.getFilePointer();
+                        out.writeBytes("<entry>\n");
+                    } catch (Exception ex) {
+                    }
+                }
+
+                String seqName = parseElement(result[r], "<name>", out);
+                sequence = align.findName(seqName);
+
+                if (sequence == null) {
+                    sequence = align.findName(seqName.substring(0,
+                                seqName.indexOf('_')));
+
+                    if (sequence != null) {
+                        sbuffer.append("changing " + sequence.getName() +
+                            " to " + seqName + "\n");
+                        sequence.setName(seqName);
+                    }
+                }
+
+                if (sequence == null) {
+                    sbuffer.append("UNIPROT updated suggestion is " +
+                        result[r] + "\n");
+                    sequence = align.findName(result[r]);
+
+                    // this entry has been suggested by ebi.
+                    // doesn't match id in alignment file
+                    try {
+                        out.setLength(filePointer);
+                    } catch (Exception ex) {
+                    }
+
+                    // now skip to next entry
+                    while (result[r].indexOf("</entry>") == -1)
+                        r++;
+                }
+
+                features = new Vector();
+                type = "";
+                start = "0";
+                end = "0";
+                description = "";
+                status = "";
+                pdb = "";
+            }
+
+            if (sequence == null) {
+                continue;
+            }
+
+            if (result[r].indexOf("<property type=\"pdb accession\"") > -1) {
+                pdb = parseValue(result[r], "value=", out);
+                sequence.setPDBId(pdb);
+            }
+
+            if (result[r].indexOf("feature type") > -1) {
+                type = parseValue(result[r], "type=", out);
+                description = parseValue(result[r], "description=", null);
+                status = parseValue(result[r], "status=", null);
+
+                while (result[r].indexOf("position") == -1) {
+                    r++; //<location>
+                }
+
+                // r++;
+                if (result[r].indexOf("begin") > -1) {
+                    start = parseValue(result[r], "position=", out);
+                    end = parseValue(result[++r], "position=", out);
+                } else {
+                    start = parseValue(result[r], "position=", out);
+                    end = parseValue(result[r], "position=", null);
+                }
+
+                int sstart = Integer.parseInt(start);
+                int eend = Integer.parseInt(end);
+
+                if (out != null) {
+                    try {
+                        out.writeBytes("</feature>\n");
+                    } catch (Exception ex) {
+                    }
+                }
+
+                SequenceFeature sf = new SequenceFeature(type, sstart, eend,
+                        description, status);
+                features.add(sf);
+            }
+
+            if (result[r].indexOf("<sequence") > -1) {
+                StringBuffer seqString = new StringBuffer();
+
+                if (out != null) {
+                    try {
+                        out.writeBytes(result[r] + "\n");
+                    } catch (Exception ex) {
+                    }
+                }
+
+                while (result[++r].indexOf("</sequence>") == -1) {
+                    seqString.append(result[r]);
+
+                    if (out != null) {
+                        try {
+                            out.writeBytes(result[r] + "\n");
+                        } catch (Exception ex) {
+                        }
+                    }
+                }
+
+                if (out != null) {
+                    try {
+                        out.writeBytes(result[r] + "\n");
+                    } catch (Exception ex) {
+                    }
+                }
+
+                StringBuffer nonGapped = new StringBuffer();
+
+                for (int i = 0; i < sequence.getSequence().length(); i++) {
+                    if (!jalview.util.Comparison.isGap(sequence.getCharAt(i))) {
+                        nonGapped.append(sequence.getCharAt(i));
+                    }
+                }
+
+                int absStart = seqString.toString().indexOf(nonGapped.toString());
+
+                if (absStart == -1) {
+                    unknownSequences.add(sequence.getName());
+                    features = null;
+                    sbuffer.append(sequence.getName() +
+                        " SEQUENCE NOT %100 MATCH \n");
+
+                    continue;
+                }
+
+                int absEnd = absStart + nonGapped.toString().length();
+                absStart += 1;
+
+                if ((absStart != sequence.getStart()) ||
+                        (absEnd != sequence.getEnd())) {
+                    sbuffer.append("Updated: " + sequence.getName() + " " +
+                        sequence.getStart() + "/" + sequence.getEnd() +
+                        "  to  " + absStart + "/" + absEnd + "\n");
+                }
+
+                sequence.setStart(absStart);
+                sequence.setEnd(absEnd);
+            }
+
+            if (result[r].indexOf("</entry>") > -1) {
+                if (features != null) {
+                    sequence.setSequenceFeatures(features);
+                }
+
+                features = null;
+                sequence = null;
+
+                if (out != null) {
+                    try {
+                        out.writeBytes("</entry>\n");
+                    } catch (Exception ex) {
+                    }
+                }
+            }
+        }
+    }
 
-void findMissingIds(AlignmentI align)
-{
-  String data;
-  ArrayList cachedIds = new ArrayList();
-
-  try
-  {
-    BufferedReader in = new BufferedReader(
-        new FileReader(jalview.bin.Cache.getProperty("UNIPROT_CACHE")));
-
-    while ( (data = in.readLine()) != null)
-    {
-      if (data.indexOf("name") > -1)
-      {
-        String name = parseElement(data, "<name>", null);
-        cachedIds.add(name);
-      }
+    void findMissingIds(AlignmentI align) {
+        String data;
+        ArrayList cachedIds = new ArrayList();
+
+        try {
+            BufferedReader in = new BufferedReader(new FileReader(
+                        jalview.bin.Cache.getProperty("UNIPROT_CACHE")));
+
+            while ((data = in.readLine()) != null) {
+                if (data.indexOf("name") > -1) {
+                    String name = parseElement(data, "<name>", null);
+                    cachedIds.add(name);
+                }
+            }
+        } catch (Exception ex) {
+            ex.printStackTrace();
+        }
+
+        for (int i = 0; i < align.getHeight(); i++)
+            if (!cachedIds.contains(align.getSequenceAt(i).getName())) {
+                unknownSequences.add(align.getSequenceAt(i).getName());
+            }
     }
-  }
-  catch (Exception ex)
-  {   ex.printStackTrace();  }
 
-  for(int i=0; i<align.getHeight(); i++)
-    if( !cachedIds.contains( align.getSequenceAt(i).getName() ) )
-      unknownSequences.add( align.getSequenceAt(i).getName() );
+    void tryLocalCacheFirst(ArrayList ids, AlignmentI align) {
+        ArrayList cacheData = new ArrayList();
 
+        try {
+            BufferedReader in = new BufferedReader(new FileReader(
+                        jalview.bin.Cache.getProperty("UNIPROT_CACHE")));
 
-}
+            // read through cache file, if the cache has sequences we're looking for
+            // add the lines to a new String array, Readthis new array and
+            // make sure we remove the ids from the list to retrieve from EBI
+            String data;
 
-void tryLocalCacheFirst(ArrayList ids, AlignmentI align)
-{
-  ArrayList cacheData = new ArrayList();
-  try{
-    BufferedReader in = new BufferedReader(
-          new FileReader(jalview.bin.Cache.getProperty("UNIPROT_CACHE")));
-
-    // read through cache file, if the cache has sequences we're looking for
-    // add the lines to a new String array, Readthis new array and
-    // make sure we remove the ids from the list to retrieve from EBI
-    String data;
-    while( ( data=in.readLine())!=null)
-    {
-      if(data.indexOf("name")>-1)
-      {
-        String name = parseElement( data, "<name>" , null) ;
-        if(ids.contains( name ) )
-        {
-          cacheData.add("<entry>");
-          cacheData.add(data);
-          while( data.indexOf("</entry>")==-1)
-          {
-            data = in.readLine();
-            cacheData.add(data);
-          }
-          cacheData.add(data);
-
-          ids.remove( name );
-        }
-      }
-    }
-  }
-  catch(Exception ex){ex.printStackTrace();}
+            while ((data = in.readLine()) != null) {
+                if (data.indexOf("name") > -1) {
+                    String name = parseElement(data, "<name>", null);
 
-  String [] localData = new String[cacheData.size()];
-  cacheData.toArray( localData );
-  if(localData!=null && localData.length>0)
-    ReadUniprotFile(localData, null, align);
-}
+                    if (ids.contains(name)) {
+                        cacheData.add("<entry>");
+                        cacheData.add(data);
 
+                        while (data.indexOf("</entry>") == -1) {
+                            data = in.readLine();
+                            cacheData.add(data);
+                        }
 
-String parseValue(String line, String tag, RandomAccessFile out)
-{
-  if(out!=null)
-    try{  out.writeBytes(line+"\n"); }catch(Exception ex){}
+                        cacheData.add(data);
 
+                        ids.remove(name);
+                    }
+                }
+            }
+        } catch (Exception ex) {
+            ex.printStackTrace();
+        }
 
-  int index = line.indexOf(tag)+tag.length()+1;
-  if(index==tag.length())
-    return "";
+        String[] localData = new String[cacheData.size()];
+        cacheData.toArray(localData);
 
-  return line.substring( index, line.indexOf("\"", index+1) );
-}
+        if ((localData != null) && (localData.length > 0)) {
+            ReadUniprotFile(localData, null, align);
+        }
+    }
+
+    String parseValue(String line, String tag, RandomAccessFile out) {
+        if (out != null) {
+            try {
+                out.writeBytes(line + "\n");
+            } catch (Exception ex) {
+            }
+        }
 
+        int index = line.indexOf(tag) + tag.length() + 1;
 
-String parseElement(String line, String tag, RandomAccessFile out)
-{
-  if (out != null)
-    try
-    {
-      out.writeBytes(line + "\n");
+        if (index == tag.length()) {
+            return "";
+        }
+
+        return line.substring(index, line.indexOf("\"", index + 1));
     }
-    catch (Exception ex)
-    {}
 
-  int index = line.indexOf(tag) + tag.length();
-  return line.substring(index, line.indexOf("</"));
+    String parseElement(String line, String tag, RandomAccessFile out) {
+        if (out != null) {
+            try {
+                out.writeBytes(line + "\n");
+            } catch (Exception ex) {
+            }
+        }
 
-  }
+        int index = line.indexOf(tag) + tag.length();
+
+        return line.substring(index, line.indexOf("</"));
+    }
 }