X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=aeb48008f51fa8350fd56f54b6ff7dc3aded716a;hb=7243db3d99cc1760c2d4802f3005b4f86d1b4bd6;hp=c1c586a3e4c0dff15e4d31f8f2bd02dead1b924b;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index c1c586a..aeb4800 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,20 +1,19 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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 .
*/
package MCview;
@@ -48,6 +47,8 @@ public class PDBChain
public Sequence sequence;
+ public boolean isNa = false;
+
public boolean isVisible = true;
public int pdbstart = 0;
@@ -66,6 +67,21 @@ public class PDBChain
this.id = id;
}
+ /**
+ * character used to write newlines
+ */
+ protected String newline = System.getProperty("line.separator");
+
+ public void setNewlineString(String nl)
+ {
+ newline = nl;
+ }
+
+ public String getNewlineString()
+ {
+ return newline;
+ }
+
public String print()
{
String tmp = "";
@@ -74,17 +90,28 @@ public class PDBChain
{
tmp = tmp + ((Bond) bonds.elementAt(i)).at1.resName + " "
+ ((Bond) bonds.elementAt(i)).at1.resNumber + " " + offset
- + "\n";
+ + newline;
}
return tmp;
}
+ /**
+ * Annotate the residues with their corresponding positions in s1 using the
+ * alignment in as
+ * NOTE: This clears all atom.alignmentMapping values on the structure.
+ * @param as
+ * @param s1
+ */
public void makeExactMapping(AlignSeq as, SequenceI s1)
{
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;
+ }
+ // and now trace the alignment onto the atom set.
for (int i = 0; i < as.astr1.length(); i++)
{
if (as.astr1.charAt(i) != '-')
@@ -116,7 +143,7 @@ public class PDBChain
*
* @param seq
* @param status
- * The Status of the transferred annotation
+ * The Status of the transferred annotation
* @return the features added to sq (or its dataset)
*/
public SequenceFeature[] transferRESNUMFeatures(SequenceI seq,
@@ -134,8 +161,8 @@ public class PDBChain
/**
* Remove any existing features for this chain if they exist ?
* SequenceFeature[] seqsfeatures=seq.getSequenceFeatures(); int
- * totfeat=seqsfeatures.length; // Remove any features for this exact chain ?
- * for (int i=0; i 0 && ((numNa / residues.size()) > 0.99))
+ {
+ isNa = true;
+ }
}
public void makeBond(Atom at1, Atom at2)
@@ -204,6 +246,9 @@ public class PDBChain
public void makeResidueList()
{
int count = 0;
+ Object symbol;
+ boolean deoxyn=false;
+ boolean nucleotide = false;
StringBuffer seq = new StringBuffer();
Vector resFeatures = new Vector();
Vector resAnnotation = new Vector();
@@ -250,22 +295,37 @@ public class PDBChain
SequenceFeature sf = new SequenceFeature("RESNUM", tmpat.resName
+ ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
+ count, offset + count, pdbid);
-
// MCview.PDBChain.PDBFILEFEATURE);
resFeatures.addElement(sf);
resAnnotation.addElement(new Annotation(tmpat.tfactor));
// Keep totting up the sequence
- if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null)
+ if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
{
- seq.append("X");
- // System.err.println("PDBReader:Null aa3Hash for " +
- // tmpat.resName);
+ 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'];
+ if (tmpat.name.equalsIgnoreCase("CA")
+ || ResidueProperties.nucleotideIndex[nucname.charAt((deoxyn ? 1 : 0))] == -1)
+ {
+ seq.append("X");
+ // System.err.println("PDBReader:Null aa3Hash for " +
+ // tmpat.resName);
+ }
+ else
+ {
+ // nucleotide flag
+ nucleotide = true;
+ seq.append(nucname.charAt((deoxyn ? 1 : 0)));
+ }
}
else
{
-
- seq.append(ResidueProperties.aa[((Integer) ResidueProperties
- .getAA3Hash().get(tmpat.resName)).intValue()]);
+ if (nucleotide)
+ {
+ System.err
+ .println("Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!");
+ }
+ seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]);
}
count++;
}
@@ -274,11 +334,14 @@ public class PDBChain
{
id = " ";
}
-
+ isNa = nucleotide;
sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note:
- // resNumber-offset
- // ~=
- // seq.size()
+ // resNumber-offset
+ // ~=
+ // seq.size()
+ // Add normalised feature scores to RESNUM indicating start/end of sequence
+ // sf.setScore(offset+count);
+
// System.out.println("PDB Sequence is :\nSequence = " + seq);
// System.out.println("No of residues = " + residues.size());
for (i = 0, iSize = resFeatures.size(); i < iSize; i++)
@@ -297,7 +360,7 @@ public class PDBChain
resAnnotation.setElementAt(null, i);
}
AlignmentAnnotation tfactorann = new AlignmentAnnotation(
- "PDB.CATempFactor", "CA Temperature Factor for "
+ "PDB.TempFactor", "Temperature Factor for "
+ sequence.getName(), annots, 0, max,
AlignmentAnnotation.LINE_GRAPH);
tfactorann.setSequenceRef(sequence);
@@ -443,11 +506,9 @@ public class PDBChain
}
}
}
- sq
- .addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
- "PDB Residue Numbering for " + this.pdbid + ":"
- + this.id, an, (float) min, (float) 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));
}
}
}