X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=ebc52aaf0aa0643410590de2c330fd5611782160;hb=3729618c7df9803178a79112efe65bd4f08779ea;hp=44bf1bcc0092163bb03ebfaec92f8ce4403cebcd;hpb=e5127e5f27f02c8f328539eaac68eabfbee1d135;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 44bf1bc..ebc52aa 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,145 +1,257 @@
-package MCview;
-
-import jalview.datamodel.*;
-import java.io.*;
-import java.net.*;
-import java.util.*;
-
-
-public class PDBfile extends jalview.io.FileParse {
-
-  public Vector chains = new Vector();
-
-  Vector lineArray = new Vector();
-
-  public PDBfile(String [] lines)
-  {
-    for(int i=0; i<lines.length; i++)
-      lineArray.addElement(lines[i]);
-
-    noLines = lineArray.size();
-    parse();
-  }
-
-  public PDBfile(String inFile, String inType) throws IOException {
-
-    super(inFile,inType);
-
-    String line;
-    this.lineArray = new Vector();
-    BufferedReader dataIn;
-
-    if (inType.equals("File"))
-      dataIn =  new BufferedReader(new FileReader( inFile ));
-
-    else
-    {
-      URL url = new URL(inFile);
-      this.fileSize = 0;
-      dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
-    }
-
-    while ((line = dataIn.readLine()) != null) {
-      lineArray.addElement(line);
-    }
-    noLines = lineArray.size();
-
-    parse();
-
-}
-
-
-  public void parse() {
-
-    for (int i = 0; i < lineArray.size(); i++) {
-      StringTokenizer str = new StringTokenizer(lineArray.elementAt(i).toString());
-      if (str.hasMoreTokens()) {
-        String inStr = str.nextToken();
-
-        if (inStr.indexOf("ATOM") != -1) {
-          try {
-            myAtom tmpatom = new myAtom(str);
-            if (findChain(tmpatom.chain) != null) {
-           //   System.out.println("Adding to chain " + tmpatom.chain);
-              findChain(tmpatom.chain).atoms.addElement(tmpatom);
-            } else {
-            //  System.out.println("Making chain " + tmpatom.chain);
-              PDBChain tmpchain = new PDBChain(tmpatom.chain);
-              chains.addElement(tmpchain);
-              tmpchain.atoms.addElement(tmpatom);
-            }
-          } catch(NumberFormatException e) {
-            System.err.println("Caught" +  e);
-            System.err.println("Record not added to PDB model:"+lineArray.elementAt(i).toString());
-          }
-        }
-      }
-    }
-    makeResidueList();
-    makeCaBondList();
-    //    for (int i=0; i < chains.size() ; i++) {
-    //  String pog = ((PDBChain)chains.elementAt(i)).print();
-    //  System.out.println(pog);
-    // }
-  }
-
-  public void makeResidueList() {
-    for (int i=0; i < chains.size() ; i++) {
-      ((PDBChain)chains.elementAt(i)).makeResidueList();
-    }
-  }
-  public void makeCaBondList() {
-    for (int i=0; i < chains.size() ; i++) {
-      ((PDBChain)chains.elementAt(i)).makeCaBondList();
-    }
-  }
-
-  public PDBChain findChain(String id) {
-    for (int i=0; i < chains.size(); i++) {
-      // System.out.println("ID = " + id + " " +((PDBChain)chains.elementAt(i)).id);
-      if (((PDBChain)chains.elementAt(i)).id.equals(id)) {
-        return (PDBChain)chains.elementAt(i);
-      }
-    }
-    return null;
-  }
-
-
-  public void setChargeColours() {
-    for (int i=0; i < chains.size(); i++) {
-      ((PDBChain)chains.elementAt(i)).setChargeColours();
-    }
-  }
-
-  public void setHydrophobicityColours() {
-    for (int i=0; i < chains.size(); i++) {
-      ((PDBChain)chains.elementAt(i)).setHydrophobicityColours();
-    }
-  }
-
-  public void colourBySequence(Sequence seq) {
-//SMJS TODO
-//    int max = seq.maxchain;
-//    if (seq.maxchain != -1) {
-//      ((PDBChain)chains.elementAt(max)).colourBySequence(seq);
-//    }
-  }
-
-  public void setChainColours() {
-    for (int i=0; i < chains.size(); i++) {
-      ((PDBChain)chains.elementAt(i)).setChainColours();
-    }
-  }
-  public static void main(String[] args) {
-    try {
-      PDBfile pdb = new PDBfile("enkp1.pdb","File");
-    } catch(IOException e) {
-      System.out.println(e);
-      e.printStackTrace();
-      System.exit(0);
-    }
-  }
-}
-
-
-
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package MCview;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.StructureFile;
+import jalview.util.MessageManager;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+public class PDBfile extends StructureFile
+{
+  private static String CALC_ID_PREFIX = "JalviewPDB";
+
+  public PDBfile(boolean addAlignmentAnnotations,
+          boolean predictSecondaryStructure, boolean externalSecStr)
+  {
+    super();
+    addSettings(addAlignmentAnnotations, predictSecondaryStructure,
+            externalSecStr);
+  }
+
+  public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+          boolean externalSecStr, String dataObject,
+          DataSourceType sourceType) throws IOException
+  {
+    super(false, dataObject, sourceType);
+    addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
+    doParse();
+  }
+
+  public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+          boolean externalSecStr, FileParse source) throws IOException
+  {
+    super(false, source);
+    addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
+    doParse();
+  }
+
+  @Override
+  public String print(SequenceI[] seqs, boolean jvSuffix)
+  {
+    return null;
+  }
+
+  @Override
+  public void parse() throws IOException
+  {
+    setDbRefType(DBRefSource.PDB);
+    // TODO set the filename sensibly - try using data source name.
+    setId(safeName(getDataName()));
+
+    setChains(new Vector<PDBChain>());
+    List<SequenceI> rna = new ArrayList<SequenceI>();
+    List<SequenceI> prot = new ArrayList<SequenceI>();
+    PDBChain tmpchain;
+    String line = null;
+    boolean modelFlag = false;
+    boolean terFlag = false;
+    String lastID = "";
+
+    int indexx = 0;
+    String atomnam = null;
+    try
+    {
+      while ((line = nextLine()) != null)
+      {
+        if (line.indexOf("HEADER") == 0)
+        {
+          if (line.length() > 62)
+          {
+            String tid;
+            if (line.length() > 67)
+            {
+              tid = line.substring(62, 67).trim();
+            }
+            else
+            {
+              tid = line.substring(62).trim();
+            }
+            if (tid.length() > 0)
+            {
+              setId(tid);
+            }
+            continue;
+          }
+        }
+        // Were we to do anything with SEQRES - we start it here
+        if (line.indexOf("SEQRES") == 0)
+        {
+        }
+
+        if (line.indexOf("MODEL") == 0)
+        {
+          modelFlag = true;
+        }
+
+        if (line.indexOf("TER") == 0)
+        {
+          terFlag = true;
+        }
+
+        if (modelFlag && line.indexOf("ENDMDL") == 0)
+        {
+          break;
+        }
+        if (line.indexOf("ATOM") == 0
+                || (line.indexOf("HETATM") == 0 && !terFlag))
+        {
+          terFlag = false;
+
+          // Jalview is only interested in CA bonds????
+          atomnam = line.substring(12, 15).trim();
+          if (!atomnam.equals("CA") && !atomnam.equals("P"))
+          {
+            continue;
+          }
+
+          Atom tmpatom = new Atom(line);
+          try
+          {
+            tmpchain = findChain(tmpatom.chain);
+            if (tmpatom.resNumIns.trim().equals(lastID))
+            {
+              // phosphorylated protein - seen both CA and P..
+              continue;
+            }
+            tmpchain.atoms.addElement(tmpatom);
+          } catch (Exception e)
+          {
+            tmpchain = new PDBChain(getId(), tmpatom.chain);
+            getChains().add(tmpchain);
+            tmpchain.atoms.addElement(tmpatom);
+          }
+          lastID = tmpatom.resNumIns.trim();
+        }
+        index++;
+      }
+
+      makeResidueList();
+      makeCaBondList();
+
+      if (getId() == null)
+      {
+        setId(inFile.getName());
+      }
+      for (PDBChain chain : getChains())
+      {
+        SequenceI chainseq = postProcessChain(chain);
+        if (isRNA(chainseq))
+        {
+          rna.add(chainseq);
+        }
+        else
+        {
+          prot.add(chainseq);
+        }
+      }
+      if (predictSecondaryStructure)
+      {
+        addSecondaryStructure(rna, prot);
+      }
+    } catch (OutOfMemoryError er)
+    {
+      System.out.println("OUT OF MEMORY LOADING PDB FILE");
+      throw new IOException(MessageManager
+              .getString("exception.outofmemory_loading_pdb_file"));
+    } catch (NumberFormatException ex)
+    {
+      if (line != null)
+      {
+        System.err.println("Couldn't read number from line:");
+        System.err.println(line);
+      }
+    }
+    markCalcIds();
+  }
+
+  /**
+   * Process a parsed chain to construct and return a Sequence, and add it to
+   * the list of sequences parsed.
+   * 
+   * @param chain
+   * @return
+   */
+
+  public static boolean isCalcIdHandled(String calcId)
+  {
+    return calcId != null && (CALC_ID_PREFIX.equals(calcId));
+  }
+
+  public static boolean isCalcIdForFile(AlignmentAnnotation alan,
+          String pdbFile)
+  {
+    return alan.getCalcId() != null
+            && CALC_ID_PREFIX.equals(alan.getCalcId())
+            && pdbFile.equals(alan.getProperty("PDBID"));
+  }
+
+  public static String relocateCalcId(String calcId,
+          Hashtable<String, String> alreadyLoadedPDB) throws Exception
+  {
+    int s = CALC_ID_PREFIX.length(),
+            end = calcId.indexOf(CALC_ID_PREFIX, s);
+    String between = calcId.substring(s, end - 1);
+    return CALC_ID_PREFIX + alreadyLoadedPDB.get(between) + ":"
+            + calcId.substring(end);
+  }
+
+  private void markCalcIds()
+  {
+    for (SequenceI sq : seqs)
+    {
+      if (sq.getAnnotation() != null)
+      {
+        for (AlignmentAnnotation aa : sq.getAnnotation())
+        {
+          String oldId = aa.getCalcId();
+          if (oldId == null)
+          {
+            oldId = "";
+          }
+          aa.setCalcId(CALC_ID_PREFIX);
+          aa.setProperty("PDBID", getId());
+          aa.setProperty("oldCalcId", oldId);
+        }
+      }
+    }
+  }
+
+}