X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fmc_view%2FPDBChain.java;h=035e60899ca84797b8cfd8b23c3247b9ab64b5ab;hb=3158d6fc128da5a06e30446e8eabb4afa9c53cb6;hp=e1c90f3cc9fc58fcba20c9d6d6e552c7b479bea1;hpb=75aa2f504257f5564e3a88c3677905d7c392f24e;p=jalview.git

diff --git a/src/mc_view/PDBChain.java b/src/mc_view/PDBChain.java
index e1c90f3..035e608 100755
--- a/src/mc_view/PDBChain.java
+++ b/src/mc_view/PDBChain.java
@@ -20,23 +20,26 @@
  */
 package mc_view;
 
+import java.awt.Color;
+import java.util.List;
+import java.util.Locale;
+import java.util.Vector;
+
 import jalview.analysis.AlignSeq;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.annotations.AnnotationRowBuilder;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureImportSettings;
 import jalview.structure.StructureMapping;
 import jalview.util.Comparison;
 
-import java.awt.Color;
-import java.util.List;
-import java.util.Vector;
-
 public class PDBChain
 {
   public static final String RESNUM_FEATURE = "RESNUM";
@@ -78,27 +81,31 @@ public class PDBChain
 
   public String pdbid = "";
 
-  String tfacName = "Temperature Factor";
-
+  AnnotationRowBuilder tfacTemplate = new AnnotationRowBuilder(
+          "TemperatureFactor");
 
-  public PDBChain(String thePdbid, String theId, String tempFactorColumnName)
+  public PDBChain(String thePdbid, String theId,
+          AnnotationRowBuilder template)
   {
-    this.pdbid = thePdbid == null ? thePdbid : thePdbid.toLowerCase();
-    this.id = theId;
-    if (tempFactorColumnName!=null && tempFactorColumnName.length()>0)
+    this(thePdbid, theId);
+    if (template != null)
     {
-      tfacName = tempFactorColumnName;
+      tfacTemplate = template;
     }
   }
 
   /**
-   * import chain data assuming Temperature Factor is in the Temperature Factor column
+   * import chain data assuming Temperature Factor is in the Temperature Factor
+   * column
+   * 
    * @param thePdbid
    * @param theId
    */
   public PDBChain(String thePdbid, String theId)
   {
-    this(thePdbid,theId, null);
+    this.pdbid = thePdbid == null ? thePdbid
+            : thePdbid.toLowerCase(Locale.ROOT);
+    this.id = theId;
   }
 
   /**
@@ -210,8 +217,8 @@ public class PDBChain
       }
       char seqchar = ds.getCharAt(seqpos - ds.getStart());
 
-      boolean sameResidue = Comparison.isSameResidue(
-              seqchar, strchar, false);
+      boolean sameResidue = Comparison.isSameResidue(seqchar, strchar,
+              false);
       if (sameResidue)
       {
         for (Atom atom : res.atoms)
@@ -229,10 +236,18 @@ public class PDBChain
    * @param seq
    * @param status
    *          The Status of the transferred annotation
+   * 
+   * @param altPDBID
+   *          the group id for the features on the destination sequence (e.g.
+   *          the official accession ID)
    */
-  public void transferRESNUMFeatures(SequenceI seq,
-          String status)
+  public void transferRESNUMFeatures(SequenceI seq, String status,
+          String altPDBID)
   {
+    if (altPDBID == null)
+    {
+      altPDBID = pdbid;
+    }
     SequenceI sq = seq;
     while (sq != null && sq.getDatasetSequence() != null)
     {
@@ -260,12 +275,13 @@ public class PDBChain
       if (feature.getFeatureGroup() != null
               && feature.getFeatureGroup().equals(pdbid))
       {
-        int newBegin = 1 + residues.elementAt(feature.getBegin() - offset).atoms
-                .elementAt(0).alignmentMapping;
+        int newBegin = 1
+                + residues.elementAt(feature.getBegin() - offset).atoms
+                        .elementAt(0).alignmentMapping;
         int newEnd = 1 + residues.elementAt(feature.getEnd() - offset).atoms
                 .elementAt(0).alignmentMapping;
         SequenceFeature tx = new SequenceFeature(feature, newBegin, newEnd,
-                feature.getFeatureGroup(), feature.getScore());
+                altPDBID, feature.getScore());
         tx.setStatus(status
                 + ((tx.getStatus() == null || tx.getStatus().length() == 0)
                         ? ""
@@ -410,8 +426,8 @@ public class PDBChain
       {
         String desc = currAtom.resName + ":" + currAtom.resNumIns + " "
                 + pdbid + id;
-        SequenceFeature sf = new SequenceFeature("INSERTION", desc, offset
-                + count - 1, offset + count - 1, "PDB_INS");
+        SequenceFeature sf = new SequenceFeature("INSERTION", desc,
+                offset + count - 1, offset + count - 1, "PDB_INS");
         resFeatures.addElement(sf);
         residues.lastElement().atoms.addAll(resAtoms);
       }
@@ -423,8 +439,8 @@ public class PDBChain
         Residue tmpres = residues.lastElement();
         Atom tmpat = tmpres.atoms.get(0);
         // Make A new SequenceFeature for the current residue numbering
-        String desc = tmpat.resName
-                + ":" + tmpat.resNumIns + " " + pdbid + id;
+        String desc = tmpat.resName + ":" + tmpat.resNumIns + " " + pdbid
+                + id;
         SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE, desc,
                 offset + count, offset + count, pdbid);
         resFeatures.addElement(sf);
@@ -503,14 +519,23 @@ public class PDBChain
       for (int i = 0; i < iSize; i++)
       {
         annots[i] = resAnnotation.elementAt(i);
+        tfacTemplate.processAnnotation(annots[i]);
         max = Math.max(max, annots[i].value);
         min = Math.min(min, annots[i].value);
         resAnnotation.setElementAt(null, i);
       }
+      if (tfacTemplate.isHasMinMax())
+      {
+        max = tfacTemplate.getMax();
+        min = tfacTemplate.getMin();
+      }
+
       AlignmentAnnotation tfactorann = new AlignmentAnnotation(
-              tfacName, tfacName + " for " + pdbid + id,
+              tfacTemplate.getName(),
+              (tfacTemplate.isHasDescription()
+                      ? tfacTemplate.getDescription()
+                      : tfacTemplate.getName()) + " for " + pdbid + id,
               annots, min, max, AlignmentAnnotation.LINE_GRAPH);
-      
       tfactorann.setCalcId(getClass().getName());
 
       tfactorann.setSequenceRef(sequence);
@@ -518,7 +543,6 @@ public class PDBChain
     }
   }
 
-
   /**
    * Colour start/end of bonds by charge
    * <ul>
@@ -641,10 +665,16 @@ public class PDBChain
                   ana.getCalcId(), ana.label, ana.description);
           if (transfer == null || transfer.size() == 0)
           {
+            ContactMatrixI cm = shadow.getContactMatrixFor(ana);
             ana = new AlignmentAnnotation(ana);
+            // TODO map contact matrix under mapping
             ana.liftOver(sequence, shadowMap);
             ana.liftOver(dsq, sqmpping);
             dsq.addAlignmentAnnotation(ana);
+            if (cm != null)
+            {
+              dsq.addContactListFor(ana, cm);
+            }
           }
           else
           {
@@ -665,10 +695,14 @@ public class PDBChain
                             ana.description);
             if (transfer == null || transfer.size() == 0)
             {
+              ContactMatrixI cm = sequence.getContactMatrixFor(ana);
               ana = new AlignmentAnnotation(ana);
               ana.liftOver(dsq, sqmpping);
               dsq.addAlignmentAnnotation(ana);
-              // mapping.transfer(ana);
+              if (cm != null)
+              {
+                dsq.addContactListFor(ana, cm);
+              }
             }
             else
             {
@@ -682,8 +716,8 @@ public class PDBChain
         // Useful for debugging mappings - adds annotation for mapped position
         float min = -1, max = 0;
         Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
-        for (int i = sq.getStart(), j = sq
-                .getEnd(), k = 0; i <= j; i++, k++)
+        for (int i = sq.getStart(), j = sq.getEnd(),
+                k = 0; i <= j; i++, k++)
         {
           int prn = mapping.getPDBResNum(k + 1);