X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=ebc52aaf0aa0643410590de2c330fd5611782160;hb=39b4859e1a1b011af5d06058461db4d075acb578;hp=691fdcd81b4f5264171cc543cc51ff674a7b438e;hpb=0df5bf86b6dea4d148a6a8fdd1f4bdce4f475fa8;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 691fdcd..ebc52aa 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,87 +20,72 @@
  */
 package MCview;
 
-import jalview.analysis.AlignSeq;
-import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.PDBEntry;
+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.awt.Color;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Vector;
 
-public class PDBfile extends jalview.io.AlignFile
+public class PDBfile extends StructureFile
 {
-  public Vector<PDBChain> chains;
+  private static String CALC_ID_PREFIX = "JalviewPDB";
 
-  public String id;
-
-  /**
-   * set to true to add chain alignment annotation as visible annotation.
-   */
-  boolean VisibleChainAnnotation = false;
-
-  boolean processSecondaryStructure = true;
-
-  boolean externalSecondaryStructure = false;
-
-  public PDBfile(boolean visibleChainAnnotation,
-          boolean processSecondaryStructure, boolean externalSecStr)
+  public PDBfile(boolean addAlignmentAnnotations,
+          boolean predictSecondaryStructure, boolean externalSecStr)
   {
     super();
-    VisibleChainAnnotation = visibleChainAnnotation;
-    this.processSecondaryStructure = processSecondaryStructure;
-    this.externalSecondaryStructure = externalSecStr;
+    addSettings(addAlignmentAnnotations, predictSecondaryStructure,
+            externalSecStr);
   }
 
-  public PDBfile(boolean visibleChainAnnotation,
-          boolean processSecondaryStructure, boolean externalSecStr,
-          String file, String protocol) throws IOException
+  public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+          boolean externalSecStr, String dataObject,
+          DataSourceType sourceType) throws IOException
   {
-    super(false, file, protocol);
-    VisibleChainAnnotation = visibleChainAnnotation;
-    this.processSecondaryStructure = processSecondaryStructure;
-    this.externalSecondaryStructure = externalSecStr;
+    super(false, dataObject, sourceType);
+    addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
     doParse();
   }
 
-  public PDBfile(boolean visibleChainAnnotation,
-          boolean processSecondaryStructure, boolean externalSecStr,
-          FileParse source) throws IOException
+  public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+          boolean externalSecStr, FileParse source) throws IOException
   {
     super(false, source);
-    VisibleChainAnnotation = visibleChainAnnotation;
-    this.processSecondaryStructure = processSecondaryStructure;
-    this.externalSecondaryStructure = externalSecStr;
+    addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
     doParse();
   }
 
-  public String print()
+  @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.
-    id = safeName(getDataName());
+    setId(safeName(getDataName()));
 
-    chains = new Vector();
-    ArrayList<SequenceI> rna = new ArrayList<SequenceI>(), prot = new ArrayList<SequenceI>();
+    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 index = 0;
+    int indexx = 0;
     String atomnam = null;
     try
     {
@@ -121,7 +106,7 @@ public class PDBfile extends jalview.io.AlignFile
             }
             if (tid.length() > 0)
             {
-              id = tid;
+              setId(tid);
             }
             continue;
           }
@@ -158,20 +143,19 @@ public class PDBfile extends jalview.io.AlignFile
           }
 
           Atom tmpatom = new Atom(line);
-          tmpchain = findChain(tmpatom.chain);
-          if (tmpchain != null)
+          try
           {
+            tmpchain = findChain(tmpatom.chain);
             if (tmpatom.resNumIns.trim().equals(lastID))
             {
               // phosphorylated protein - seen both CA and P..
               continue;
             }
             tmpchain.atoms.addElement(tmpatom);
-          }
-          else
+          } catch (Exception e)
           {
-            tmpchain = new PDBChain(id, tmpatom.chain);
-            chains.addElement(tmpchain);
+            tmpchain = new PDBChain(getId(), tmpatom.chain);
+            getChains().add(tmpchain);
             tmpchain.atoms.addElement(tmpatom);
           }
           lastID = tmpatom.resNumIns.trim();
@@ -182,36 +166,14 @@ public class PDBfile extends jalview.io.AlignFile
       makeResidueList();
       makeCaBondList();
 
-      if (id == null)
+      if (getId() == null)
       {
-        id = inFile.getName();
+        setId(inFile.getName());
       }
-      for (int i = 0; i < chains.size(); i++)
+      for (PDBChain chain : getChains())
       {
-        SequenceI dataset = chains.elementAt(i).sequence;
-        dataset.setName(id + "|" + dataset.getName());
-        PDBEntry entry = new PDBEntry();
-        entry.setId(id);
-        entry.setProperty(new Hashtable());
-        if (chains.elementAt(i).id != null)
-        {
-          entry.getProperty().put("CHAIN", chains.elementAt(i).id);
-        }
-        if (inFile != null)
-        {
-          entry.setFile(inFile.getAbsolutePath());
-        }
-        else
-        {
-          // TODO: decide if we should dump the datasource to disk
-          entry.setFile(getDataName());
-        }
-        dataset.addPDBId(entry);
-        SequenceI chainseq = dataset.deriveSequence(); // PDBChain objects
-        // maintain reference to
-        // dataset
-        seqs.addElement(chainseq);
-        if (isRNA(chainseq) == true)
+        SequenceI chainseq = postProcessChain(chain);
+        if (isRNA(chainseq))
         {
           rna.add(chainseq);
         }
@@ -219,54 +181,16 @@ public class PDBfile extends jalview.io.AlignFile
         {
           prot.add(chainseq);
         }
-
-        AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
-
-        if (chainannot != null && VisibleChainAnnotation)
-        {
-          for (int ai = 0; ai < chainannot.length; ai++)
-          {
-            chainannot[ai].visible = VisibleChainAnnotation;
-            annotations.addElement(chainannot[ai]);
-          }
-        }
       }
-      if (processSecondaryStructure)
+      if (predictSecondaryStructure)
       {
-        if (externalSecondaryStructure && rna.size() > 0)
-        {
-          try
-          {
-            processPdbFileWithAnnotate3d(rna);
-          } catch (Exception x)
-          {
-            System.err
-                    .println("Exceptions when dealing with RNA in pdb file");
-            x.printStackTrace();
-
-          }
-        }
-        ;
-        if (prot.size() > 0)
-        {
-          try
-          {
-            processPdbFileWithJmol(prot);
-          } catch (Exception x)
-          {
-            System.err
-                    .println("Exceptions from Jmol when processing data in pdb file");
-            x.printStackTrace();
-
-          }
-        }
+        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"));
+      throw new IOException(MessageManager
+              .getString("exception.outofmemory_loading_pdb_file"));
     } catch (NumberFormatException ex)
     {
       if (line != null)
@@ -278,27 +202,34 @@ public class PDBfile extends jalview.io.AlignFile
     markCalcIds();
   }
 
-  private static String calcIdPrefix = "JalviewPDB";
+  /**
+   * 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 && (calcIdPrefix.equals(calcId));
+    return calcId != null && (CALC_ID_PREFIX.equals(calcId));
   }
 
   public static boolean isCalcIdForFile(AlignmentAnnotation alan,
           String pdbFile)
   {
     return alan.getCalcId() != null
-            && calcIdPrefix.equals(alan.getCalcId())
+            && 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 = calcIdPrefix.length(), end = calcId.indexOf(calcIdPrefix, s);
+    int s = CALC_ID_PREFIX.length(),
+            end = calcId.indexOf(CALC_ID_PREFIX, s);
     String between = calcId.substring(s, end - 1);
-    return calcIdPrefix + alreadyLoadedPDB.get(between) + ":"
+    return CALC_ID_PREFIX + alreadyLoadedPDB.get(between) + ":"
             + calcId.substring(end);
   }
 
@@ -315,206 +246,12 @@ public class PDBfile extends jalview.io.AlignFile
           {
             oldId = "";
           }
-          aa.setCalcId(calcIdPrefix);
-          aa.setProperty("PDBID", id);
+          aa.setCalcId(CALC_ID_PREFIX);
+          aa.setProperty("PDBID", getId());
           aa.setProperty("oldCalcId", oldId);
         }
       }
     }
   }
 
-  private void processPdbFileWithJmol(ArrayList<SequenceI> prot)
-          throws Exception
-  {
-    try
-    {
-      Class cl = Class.forName("jalview.ext.jmol.PDBFileWithJmol");
-      if (cl != null)
-      {
-        Object jmf = cl.getConstructor(new Class[]
-        { FileParse.class }).newInstance(new Object[]
-        { new FileParse(getDataName(), type) });
-        Alignment al = new Alignment((SequenceI[]) cl.getMethod(
-                "getSeqsAsArray", new Class[]
-                {}).invoke(jmf));
-        cl.getMethod("addAnnotations", new Class[]
-        { Alignment.class }).invoke(jmf, al);
-        for (SequenceI sq : al.getSequences())
-        {
-          if (sq.getDatasetSequence() != null)
-          {
-            sq.getDatasetSequence().getPDBId().clear();
-          }
-          else
-          {
-            sq.getPDBId().clear();
-          }
-        }
-        replaceAndUpdateChains(prot, al, AlignSeq.PEP, false);
-      }
-    } catch (ClassNotFoundException q)
-    {
-    }
-  }
-
-  private void replaceAndUpdateChains(ArrayList<SequenceI> prot,
-          AlignmentI al, String pep, boolean b)
-  {
-    List<List<? extends Object>> replaced = AlignSeq
-            .replaceMatchingSeqsWith(seqs, annotations, prot, al, pep,
-                    false);
-    for (PDBChain ch : chains)
-    {
-      int p = 0;
-      for (SequenceI sq : (List<SequenceI>) replaced.get(0))
-      {
-        p++;
-        if (sq == ch.sequence || sq.getDatasetSequence() == ch.sequence)
-        {
-          p = -p;
-          break;
-        }
-      }
-      if (p < 0)
-      {
-        p = -p - 1;
-        // set shadow entry for chains
-        ch.shadow = (SequenceI) replaced.get(1).get(p);
-        ch.shadowMap = ((AlignSeq) replaced.get(2).get(p))
-                .getMappingFromS1(false);
-      }
-    }
-  }
-
-  private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna)
-          throws Exception
-  {
-    // System.out.println("this is a PDB format and RNA sequence");
-    // note: we use reflection here so that the applet can compile and run
-    // without the HTTPClient bits and pieces needed for accessing Annotate3D
-    // web service
-    try
-    {
-      Class cl = Class.forName("jalview.ws.jws1.Annotate3D");
-      if (cl != null)
-      {
-        // TODO: use the PDB ID of the structure if one is available, to save
-        // bandwidth and avoid uploading the whole structure to the service
-        Object annotate3d = cl.getConstructor(new Class[]
-        {}).newInstance(new Object[]
-        {});
-        AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor",
-                new Class[]
-                { FileParse.class }).invoke(annotate3d, new Object[]
-        { new FileParse(getDataName(), type) }));
-        for (SequenceI sq : al.getSequences())
-        {
-          if (sq.getDatasetSequence() != null)
-          {
-            if (sq.getDatasetSequence().getPDBId() != null)
-            {
-              sq.getDatasetSequence().getPDBId().clear();
-            }
-          }
-          else
-          {
-            if (sq.getPDBId() != null)
-            {
-              sq.getPDBId().clear();
-            }
-          }
-        }
-        replaceAndUpdateChains(rna, al, AlignSeq.DNA, false);
-      }
-    } catch (ClassNotFoundException x)
-    {
-      // ignore classnotfounds - occurs in applet
-    }
-    ;
-  }
-
-  /**
-   * make a friendly ID string.
-   * 
-   * @param dataName
-   * @return truncated dataName to after last '/'
-   */
-  private String safeName(String dataName)
-  {
-    int p = 0;
-    while ((p = dataName.indexOf("/")) > -1 && p < dataName.length())
-    {
-      dataName = dataName.substring(p + 1);
-    }
-    return dataName;
-  }
-
-  public void makeResidueList()
-  {
-    for (int i = 0; i < chains.size(); i++)
-    {
-      chains.elementAt(i).makeResidueList(VisibleChainAnnotation);
-    }
-  }
-
-  public void makeCaBondList()
-  {
-    for (int i = 0; i < chains.size(); i++)
-    {
-      chains.elementAt(i).makeCaBondList();
-    }
-  }
-
-  public PDBChain findChain(String id)
-  {
-    for (int i = 0; i < chains.size(); i++)
-    {
-      if (chains.elementAt(i).id.equals(id))
-      {
-        return chains.elementAt(i);
-      }
-    }
-
-    return null;
-  }
-
-  public void setChargeColours()
-  {
-    for (int i = 0; i < chains.size(); i++)
-    {
-      chains.elementAt(i).setChargeColours();
-    }
-  }
-
-  public void setColours(jalview.schemes.ColourSchemeI cs)
-  {
-    for (int i = 0; i < chains.size(); i++)
-    {
-      chains.elementAt(i).setChainColours(cs);
-    }
-  }
-
-  public void setChainColours()
-  {
-    for (int i = 0; i < chains.size(); i++)
-    {
-      chains.elementAt(i).setChainColours(
-              Color.getHSBColor(1.0f / i, .4f, 1.0f));
-    }
-  }
-
-  public boolean isRNA(SequenceI seqs)
-  {
-    for (int i = 0; i < seqs.getLength(); i++)
-    {
-      if ((seqs.getCharAt(i) != 'A') && (seqs.getCharAt(i) != 'C')
-              && (seqs.getCharAt(i) != 'G') && (seqs.getCharAt(i) != 'U'))
-      {
-        return false;
-      }
-    }
-
-    return true;
-
-  }
 }