X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=47ed1ef33b7eb93b6930004369fd9495b63d23f7;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=65504e4bdebcfec7077acedced1811dd6700c6a9;hpb=f5db0ff259cbb1132f6c061615d912b0668fd728;p=jalview.git
diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 65504e4..47ed1ef 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,31 +1,40 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.
- *
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
import jalview.structure.StructureMapping;
+import java.awt.Color;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
+
public class PDBChain
{
/**
@@ -45,7 +54,16 @@ public class PDBChain
public int offset;
- public Sequence sequence;
+ /**
+ * sequence is the sequence extracted by the chain parsing code
+ */
+ public SequenceI sequence;
+
+ /**
+ * shadow is the sequence created by any other parsing processes (e.g. Jmol,
+ * RNAview)
+ */
+ public SequenceI shadow = null;
public boolean isNa = false;
@@ -72,6 +90,8 @@ public class PDBChain
*/
protected String newline = System.getProperty("line.separator");
+ public Mapping shadowMap;
+
public void setNewlineString(String nl)
{
newline = nl;
@@ -98,8 +118,9 @@ public class PDBChain
/**
* Annotate the residues with their corresponding positions in s1 using the
- * alignment in as
- * NOTE: This clears all atom.alignmentMapping values on the structure.
+ * alignment in as NOTE: This clears all atom.alignmentMapping values on the
+ * structure.
+ *
* @param as
* @param s1
*/
@@ -108,8 +129,9 @@ public class PDBChain
int pdbpos = as.getSeq2Start() - 2;
int alignpos = s1.getStart() + as.getSeq1Start() - 3;
// first clear out any old alignmentMapping values:
- for (Atom atom: (Vector) atoms) {
- atom.alignmentMapping=-1;
+ for (Atom atom : (Vector) atoms)
+ {
+ atom.alignmentMapping = -1;
}
// and now trace the alignment onto the atom set.
for (int i = 0; i < as.astr1.length(); i++)
@@ -182,7 +204,9 @@ public class PDBChain
+ ((tx.getStatus() == null || tx.getStatus().length() == 0) ? ""
: ":" + tx.getStatus()));
if (tx.begin != 0 && tx.end != 0)
+ {
sq.addSequenceFeature(tx);
+ }
}
}
return features;
@@ -243,11 +267,11 @@ public class PDBChain
bonds.addElement(new Bond(start, end, at1, at2));
}
- public void makeResidueList()
+ public void makeResidueList(boolean visibleChainAnnotation)
{
int count = 0;
Object symbol;
- boolean deoxyn=false;
+ boolean deoxyn = false;
boolean nucleotide = false;
StringBuffer seq = new StringBuffer();
Vector resFeatures = new Vector();
@@ -270,7 +294,7 @@ public class PDBChain
// remains the same as the first atom's resNumber (res)
while ((resNumber == res) && (i < atoms.size()))
{
- resAtoms.addElement((Atom) atoms.elementAt(i));
+ resAtoms.addElement(atoms.elementAt(i));
i++;
if (i < atoms.size())
@@ -302,10 +326,13 @@ public class PDBChain
if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
{
String nucname = tmpat.resName.trim();
- // use the aaIndex rather than call 'toLower' - which would take a bit more time.
- deoxyn=nucname.length()==2 && ResidueProperties.aaIndex[nucname.charAt(0)]==ResidueProperties.aaIndex['D'];
+ // use the aaIndex rather than call 'toLower' - which would take a bit
+ // more time.
+ deoxyn = nucname.length() == 2
+ && ResidueProperties.aaIndex[nucname.charAt(0)] == ResidueProperties.aaIndex['D'];
if (tmpat.name.equalsIgnoreCase("CA")
- || ResidueProperties.nucleotideIndex[nucname.charAt((deoxyn ? 1 : 0))] == -1)
+ || ResidueProperties.nucleotideIndex[nucname
+ .charAt((deoxyn ? 1 : 0))] == -1)
{
seq.append("X");
// System.err.println("PDBReader:Null aa3Hash for " +
@@ -350,21 +377,27 @@ public class PDBChain
.elementAt(i));
resFeatures.setElementAt(null, i);
}
- Annotation[] annots = new Annotation[resAnnotation.size()];
- float max = 0;
- for (i = 0, iSize = annots.length; i < iSize; i++)
+ if (visibleChainAnnotation)
{
- annots[i] = (Annotation) resAnnotation.elementAt(i);
- if (annots[i].value > max)
- max = annots[i].value;
- resAnnotation.setElementAt(null, i);
+ Annotation[] annots = new Annotation[resAnnotation.size()];
+ float max = 0;
+ for (i = 0, iSize = annots.length; i < iSize; i++)
+ {
+ annots[i] = (Annotation) resAnnotation.elementAt(i);
+ if (annots[i].value > max)
+ {
+ max = annots[i].value;
+ }
+ resAnnotation.setElementAt(null, i);
+ }
+
+ AlignmentAnnotation tfactorann = new AlignmentAnnotation(
+ "Temperature Factor", "Temperature Factor for " + pdbid + id,
+ annots, 0, max,
+ AlignmentAnnotation.LINE_GRAPH);
+ tfactorann.setSequenceRef(sequence);
+ sequence.addAlignmentAnnotation(tfactorann);
}
- AlignmentAnnotation tfactorann = new AlignmentAnnotation(
- "PDB.TempFactor", "Temperature Factor for "
- + sequence.getName(), annots, 0, max,
- AlignmentAnnotation.LINE_GRAPH);
- tfactorann.setSequenceRef(sequence);
- sequence.addAlignmentAnnotation(tfactorann);
}
public void setChargeColours()
@@ -458,57 +491,100 @@ public class PDBChain
}
}
- public AlignmentAnnotation[] transferResidueAnnotation(SequenceI seq,
- String status)
- {
- AlignmentAnnotation[] transferred = null;
-
- return transferred;
-
- }
-
/**
* copy any sequence annotation onto the sequence mapped using the provided
* StructureMapping
*
* @param mapping
+ * - positional mapping between destination sequence and pdb resnum
+ * @param sqmpping
+ * - mapping between destination sequence and local chain
*/
- public void transferResidueAnnotation(StructureMapping mapping)
+ public void transferResidueAnnotation(
+ StructureMapping mapping, jalview.datamodel.Mapping sqmpping)
{
SequenceI sq = mapping.getSequence();
+ SequenceI dsq = sq;
if (sq != null)
{
- if (sequence != null && sequence.getAnnotation() != null)
+ while (dsq.getDatasetSequence() != null)
{
-
+ dsq = dsq.getDatasetSequence();
}
- 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++)
+ // any annotation will be transferred onto the dataset sequence
+
+ if (shadow != null && shadow.getAnnotation() != null)
{
- int prn = mapping.getPDBResNum(k + 1);
- an[k] = new Annotation((float) prn);
- if (min == -1)
+ for (AlignmentAnnotation ana : shadow.getAnnotation())
{
- min = k;
- max = k;
+ List transfer = sq.getAlignmentAnnotations(
+ ana.getCalcId(), ana.label);
+ if (transfer == null || transfer.size() == 0)
+ {
+ ana = new AlignmentAnnotation(ana);
+ ana.liftOver(sequence, shadowMap);
+ ana.liftOver(dsq, sqmpping);
+ dsq.addAlignmentAnnotation(ana);
+ }
+ else
+ {
+ continue;
+ }
}
- else
+ }
+ else
+ {
+ if (sequence != null && sequence.getAnnotation() != null)
{
- if (min > k)
+ for (AlignmentAnnotation ana : sequence.getAnnotation())
{
- min = k;
+ List transfer = sq
+ .getAlignmentAnnotations(ana.getCalcId(), ana.label);
+ if (transfer == null || transfer.size() == 0)
+ {
+ ana = new AlignmentAnnotation(ana);
+ ana.liftOver(dsq, sqmpping);
+ // mapping.transfer(ana);
+ }
+ else
+ {
+ continue;
+ }
}
- else if (max < k)
+ }
+ }
+ if (false)
+ {
+ // 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++)
+ {
+ int prn = mapping.getPDBResNum(k + 1);
+
+ an[k] = new Annotation(prn);
+ if (min == -1)
{
+ min = k;
max = k;
}
+ else
+ {
+ if (min > k)
+ {
+ min = k;
+ }
+ else if (max < k)
+ {
+ max = k;
+ }
+ }
}
+ sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
+ "PDB Residue Numbering for " + this.pdbid + ":" + this.id,
+ an, min, max, AlignmentAnnotation.LINE_GRAPH));
}
- sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
- "PDB Residue Numbering for " + this.pdbid + ":" + this.id,
- an, (float) min, (float) max, AlignmentAnnotation.LINE_GRAPH));
}
}
}