JAL-674 store ID in MCview.PDBfile calcId string, not PDB filename

[jalview.git] / src / MCview / PDBfile.java

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index bb01faf..7e37277 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -20,16 +20,21 @@
  */
 package MCview;
 
-import java.io.*;
-import java.util.*;
-import java.util.List;
-import java.awt.*;
-
 import jalview.analysis.AlignSeq;
-import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
 import jalview.io.FileParse;
 import jalview.util.MessageManager;
 
+import java.awt.Color;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Vector;
+
 public class PDBfile extends jalview.io.AlignFile
 {
   public Vector chains;
@@ -215,7 +220,6 @@ public class PDBfile extends jalview.io.AlignFile
         {
           for (int ai = 0; ai < chainannot.length; ai++)
           {
-
             chainannot[ai].visible = VisibleChainAnnotation;
             annotations.addElement(chainannot[ai]);
           }
@@ -224,6 +228,7 @@ public class PDBfile extends jalview.io.AlignFile
       if (processSecondaryStructure)
       {
       if (rna.size() > 0)
+      {
         try
         {
           processPdbFileWithAnnotate3d(rna);
@@ -234,8 +239,10 @@ public class PDBfile extends jalview.io.AlignFile
           x.printStackTrace();
 
         }
+      }
       ;
       if (prot.size() > 0)
+      {
         try
         {
           processPdbFileWithJmol(prot);
@@ -247,6 +254,7 @@ public class PDBfile extends jalview.io.AlignFile
 
         }
       }
+      }
     } catch (OutOfMemoryError er)
     {
       System.out.println("OUT OF MEMORY LOADING PDB FILE");
@@ -261,8 +269,29 @@ public class PDBfile extends jalview.io.AlignFile
         System.err.println(line);
       }
     }
+    markCalcIds();
   }
 
+  public static boolean isCalcIdForFile(String calcId, String pdbFile)
+  {
+    return (calcId != null && calcId.startsWith("JalviewPDB:" + pdbFile
+            + ":JalviewPDB:"));
+  }
+  private void markCalcIds()
+  {
+    for (SequenceI sq : seqs)
+    {
+      for (AlignmentAnnotation aa : sq.getAnnotation())
+      {
+        String oldId = aa.getCalcId();
+        if (oldId == null)
+        {
+          oldId = "";
+        }
+        aa.setCalcId("JalviewPDB:" + id + ":JalviewPDB:" + oldId);
+      }
+    }
+  }
   private void processPdbFileWithJmol(ArrayList<SequenceI> prot)
           throws Exception
   {
@@ -279,7 +308,7 @@ public class PDBfile extends jalview.io.AlignFile
                 {}).invoke(jmf));
         cl.getMethod("addAnnotations", new Class[]
         { Alignment.class }).invoke(jmf, al);
-        replaceMatchingSeqsWith(seqs, annotations, prot, al, AlignSeq.PEP, false);
+        AlignSeq.replaceMatchingSeqsWith(seqs, annotations, prot, al, AlignSeq.PEP, false);
       }
     } catch (ClassNotFoundException q)
     {
@@ -307,7 +336,7 @@ public class PDBfile extends jalview.io.AlignFile
                 new Class[]
                 { FileParse.class }).invoke(annotate3d, new Object[]
         { new FileParse(getDataName(), type) }));
-        replaceMatchingSeqsWith(seqs, annotations, rna, al, AlignSeq.DNA, false);
+        AlignSeq.replaceMatchingSeqsWith(seqs, annotations, rna, al, AlignSeq.DNA, false);
       }
     } catch (ClassNotFoundException x)
     {
@@ -317,80 +346,6 @@ public class PDBfile extends jalview.io.AlignFile
   }
 
   /**
-   * matches ochains against al and populates seqs with the best match between
-   * each ochain and the set in al
-   * 
-   * @param ochains
-   * @param al
-   * @param dnaOrProtein
-   * @param removeOldAnnots when true, old annotation is cleared before new annotation transferred
-   */
-  public static void replaceMatchingSeqsWith(List<SequenceI> seqs, List<AlignmentAnnotation> annotations, List<SequenceI> ochains,
-          AlignmentI al, String dnaOrProtein, boolean removeOldAnnots)
-  {
-    if (al != null && al.getHeight() > 0)
-    {
-      ArrayList<SequenceI> matches = new ArrayList<SequenceI>();
-      ArrayList<AlignSeq> aligns = new ArrayList<AlignSeq>();
-
-      for (SequenceI sq : ochains)
-      {
-        SequenceI bestm = null;
-        AlignSeq bestaseq = null;
-        int bestscore = 0;
-        for (SequenceI msq : al.getSequences())
-        {
-          AlignSeq aseq = AlignSeq.doGlobalNWAlignment(msq, sq,
-                  dnaOrProtein);
-          if (bestm == null || aseq.getMaxScore() > bestscore)
-          {
-            bestscore = aseq.getMaxScore();
-            bestaseq = aseq;
-            bestm = msq;
-          }
-        }
-        System.out.println("Best Score for " + (matches.size() + 1) + " :"
-                + bestscore);
-        matches.add(bestm);
-        aligns.add(bestaseq);
-        al.deleteSequence(bestm);
-      }
-      for (int p = 0, pSize = seqs.size(); p < pSize; p++)
-      {
-        SequenceI sq, sp = seqs.get(p);
-        int q;
-        if ((q = ochains.indexOf(sp)) > -1)
-        {
-          seqs.set(p, sq = matches.get(q));
-          sq.setName(sp.getName());
-          sq.setDescription(sp.getDescription());
-          sq.transferAnnotation(sp, aligns.get(q).getMappingFromS1(false));
-          int inspos = -1;
-          for (int ap = 0; ap < annotations.size();)
-          {
-            if (((AlignmentAnnotation) annotations.get(ap)).sequenceRef == sp)
-            {
-              if (inspos == -1)
-              {
-                inspos = ap;
-              }
-              annotations.remove(ap);
-            }
-            else
-            {
-              ap++;
-            }
-          }
-          if (sq.getAnnotation() != null)
-          {
-            annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
-          }
-        }
-      }
-    }
-  }
-
-  /**
    * make a friendly ID string.
    * 
    * @param dataName
@@ -456,7 +411,7 @@ public class PDBfile extends jalview.io.AlignFile
     for (int i = 0; i < chains.size(); i++)
     {
       ((PDBChain) chains.elementAt(i)).setChainColours(Color.getHSBColor(
-              1.0f / (float) i, .4f, 1.0f));
+              1.0f / i, .4f, 1.0f));
     }
   }